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This is farcical. They didn't have to errata the Cargo Hold and Lighter Bay to allow Grand Cruisers to take it for the same reason they didn't have to errata the Vitae-pattern Life Sustainer to allow Grand Cruisers to take it!

The clear intent of the rule is "may use any component that a Cruiser could."* The strict reading of "cruiser-only" would restrict you to "All Ships", "Grand Cruiser", or exclusively "Cruiser"- and there are very few indeed of the latter. In fact, doing so would eliminate:

• all warp drives
• all Bridges except Ship Master's, Invasion, and Fleet Flag
• all life-sustainers
• all crew quarters
• all macrobatteries (!) except the Hecutor-Pattern Plasma Broadside
• the Titanforge and Star-Flare lances
• all lance batteries except the Godsbane
• the Jovian-Pattern Escort Bay
• all the "standard" torpedo tubes- Fortis-, Gryphonne-, and Mars-patterns.
• and literally countless supplemental components that it would be absurd to exclude, e.g. Munitorium.

thereby rendering it impossible to build a Grand Cruiser at all.

I think the error in your logic is that you interpret "cruiser-only" to include both Cruisers and Light Cruisers, and thereby permit Grand Cruisers to equip "Light Cruisers, Cruisers" parts such as the larger versions of the life-sustainers and so on. However, the entire rest of the rules treat Light Cruisers as their own class, not as part of the general "Cruiser" category for any other purpose. Even where a clear rules commonality exists, such as in the rules for prow weapon arcs, the classes are called out individually: "Prow weapons on light cruisers, cruisers, or larger vessels may fire to the fore, port, and starboard." (RT p.219). 

The strictest reading of the rules text is clearly broken and not as intended. It is far more consistent to consider the rule to permit "any component whose restrictions include Cruisers", rather than "any component whose restrictions don't include anything EXCEPT Cruisers".

*This is, itself, rather odd, as several Grand Cruisers are called out in their fluff descriptions as out of production because the Imperium no longer can- either "at all" or "practically"- produce their plasma drives. The rule really OUGHT to allow any Cruiser component except the plasma drive, or- in keeping with the precedent set by the Conquest-class Star Galleon- any Cruiser component, but if a Grand Cruiser version exists, they must use the Grand Cruiser version.

Spacedock Piers currently prevent mounting ANY weapons in Port or Starboard slots. Per Battlefleet Koronus p.40, "Due to their size, station fittings prevent any weapons with the Broadside rule from being installed (although smaller weapons may still be installed in Port and Starboard weapon capacity slots)." 

(There's also some additional weirdness going on when attempting to install Spacedock Piers while weapons are already installed in Port or Starboard weapon slots. Sometimes they'll be removed and the Spacedock Piers installed; sometimes the Spacedock Piers won't be installed, but if the weapons are then uninstalled, the Spacedock Piers magically reappear and install themselves then, and on at least one occasion the Spacedock Piers did not install, but the broadside weapons were "frozen" or "locked" somehow, and I could not uninstall or modify them- clicking them had no effect whatsoever.)

When changing the craftsmanship of most (but weirdly not all) upgrades using the drop-down menu, the description text changes to "Error: invalid Craftsmanship Rating." Once the upgrade is installed, however, the correct description text reappears.

The ability to select a Crew Rating of Elite for 25SP is homebrew/house rules of some kind; only Incompetent, Crack, or Veteran (or the default Competent) are available to the players. (Leaving the option in without an SP cost will likely still be useful to GMs creating opposing vessels.)

The Gothic- and Dominator-class Cruisers are homebrew/houserules of some kind, I believe. Their pre-equipped components do match those listed on Battlefleet Koronus p.25, but those rules simply say that those components are "equipped"- no mention is made of any inability to remove them.

 The Conquest-class Star Galleon is able to equip Transport versions of several essential components (plasma drives, warp drives, and the Mezoa Gellar-Void Integrant), where it should only be able to equip the Cruiser versions. Likewise, the dev build's non-canonical Travois has the same issue. (This may be intended, if using a more generous interpretation of the Hybrid Vessel rules that only disallows components which have different versions under the exact same component name, rather than considering them to require the Cruiser version of e.g. Plasma Drives generally, as a category. I'm not even certain it's wrong, although I've never seen it ruled this way in any of my games as either player or GM. Feel free to disregard this point.)

The Mezoa Gellar-Void Integrant can be installed on any (human) ship, rather than only Transports and Raiders.

If Background data (Past History/Machine Spirit Quirk or Background Package) is selected for a ship which should not have it (such as a xenos vessel), there is no way to clear it.

On the History screen, when Complications are selected, the Machine Spirit Quirk/Ship History pane on the right is slightly too wide; its left edge overlaps with the left pane with the selection menus and Confirm button. (This is not the case if a Background Package is selected, as its description pane is narrower.) This is the case (at varying levels of severity) on both 1080p and 4k monitors at the Windows-default UI scaling (125% and 150% respectively).

Non-canonical vessels or those not normally available to players at game start (such as the Hemlock Xenos Vessel and Retribution Battleship) should probably not list made-up SP costs.

The increased Forward armour provided by the Armoured Prow and Reinforced Prow components is not reflected on the Export Data page- adding Armoured Prow to a Lunar only shows "Armour: 20", rather than "Armour: 20 (24)". 

On the Export Data page, in the Rated Statistics panel, "Manoeuvre" is mispelled as "Manouevre". (It seems worth pointing out that the sourcebooks consistently use "Manoeuvrability" for the ship characteristic, and "Manoeuvre" for the actions and tests that characteristic adds to.)

The selection and readying of small craft wings (Fighters, Bombers, Assault Boats, Aeronautica, Support Craft) for Launch Bays could be implemented using the same system as is currently used for Torpedoes and Torpedo Tubes.

The Secondary Power Genetorium (the integral component from the Universe Mass-Conveyor) is installable on any voidship. Needless to say, +10 Power for 0 Space is both technically incorrect and a teensy little bit overpowered as fuck- and I have no idea where its supposed 2SP cost came from. The Goliath Factory Ship's Plasma Refinery has the same issue.

The xenotech Energy Drain Matrix appears incorrectly as a miscellaneous supplemental component. (It does also appear correctly, as a weapon, which is weird.)

Certain supplemental components and upgrades incorrectly can (or in two instances cannot) be equipped more than once:

• in the "Compartments" category, all appear to be correct.
• In the "Augmentations" category, the "Gilded Hull" and "Excess Void Armor" (both originally from Lure of the Expanse p.139) are listed as "Unique", and there is no indication in either the original sourcebook or the errata that this is the case. (Even if intuitively they really ought to be Unique.) 
• In the "Facilities" category, the components originally from Into the Storm are not listed as Unique; although not individually marked as unique in Table 4-3: Supplemental Components (ItS p.160), the category's rules text directly under the table makes this quite clear: "Each of the following Components may only be added to a starship once unless specified otherwise." The components in question are:
  • Arboretum
  • Asteroid Mining Facility
  • Astropathic Choir-Chambers
  • Broadband Hymn-Casters
• In the Upgrades section, all upgrades are currently able to be purchased multiple times. The only two upgrades for which this is correct are:
  • Atomics
  • Turbo-Weapon Batteries (should only be permitted once per battery, currently allows multiples)

Battle- and Grand Cruiser component restrictions are borked due to an absurd interpretation of the Grand Cruiser and Battlecruiser rules text- I already ranted about it in reply to the relevant comment somewhere below and will spare you the repetition.

The Repulsor Shield Array can be installed on Raiders, Frigates, and (non-Secutor) Light Cruisers.

Naming errors:

• The "Temple-Shrine to the God Emperor" is renamed the "Fane to the God-Emperor" for some reason. Maybe a translation error?
• All instances of "Armor" should be replaced with "Armour"; I have specifically noticed:  
  • Armor Plating (Augmentation)
  • Excess Void Armor (Augmentation)
• "Warp Drive(s)" should be "Warp Engine(s)"
• "Drive" should be "Plasma Drive" for the category label, although not for the individual drive names. 
• Nearly every "X-pattern Y" component is instead "Y; X", as are a couple other things. This is too consistent to be an error, but reads very oddly to me. If shortening the names is desirable or necessary to save space, then either "Jovian Class 4.5 "Warcruiser"" or "Class 4.5 Jovian "Warcruiser"" would read far more naturally to me than "Class 4.5; Jovian "Warcruiser"". This is only a suggestion, however.
  • However, the "Macrocannons; Thunderstrike", "Macrocannons; Mezoa", and "Torpedo Tube; Plasma-Accelerated" are not "X-pattern" and should be renamed back to "Thunderstrike Macrocannons", "Mezoa Macrocannons", and "Plasma-Accelerated Torpedo Tube" for consistency with the Jovian Missile Battery, Lathe Grav-Culverin Broadside, etc., etc.
• The "Markov Mk. 1", "Markov Mk. 2", and "Albanov Mk. 1" warp engines should be "Markov 1", "Markov 2", and "Albanov 1", respectively
• The "Mark M-1.r" life sustainer should be either "M-1.r" if you want to match the table on Rogue Trader p.201, or "Mark 1.r" if you want to match the text description on p.200.
  • Similarly, the Mark-100 and Mark-201.b augur arrays could be renamed to "M-100" and "M-201.b" if you wanted to match the table- they do correctly match the text descriptions as they are now, however.

The description text for the Markov 1 and Markov 2 Warp Engines does not reflect the errata (the Markov 1 should reduce Warp travel times by 1d10 days per week, and the Markov 2 by 1d5 days per week, unless the voyage was shorter than 1 week before this reduction. It may be further modified by the results of the Navigation(Warp) test).

The Plasma Scoop's rules (Fuel Gathering and Foolhardy Manoeuvre) have no description text, and the latter is misspelled Manoevre.

The four versions of the Mimic Engine (the xenotech plasma drive component from Hostile Acquisitions p.74(rules)/p.75(table)- not to be confused with the "Mimic Drive" Upgrade on p.77) are equipped as supplemental components in addition to the required plasma drive, rather than replacing it (i.e. being equipped as a drive). 
The Aconite Solar Sails from Lure of the Expanse p.140 have the same issue, and additionally cost 50 Power rather than generating it. 
(I should probably point out that the Aconite Solar Sail rules could be read such that they only generate power and provide propulsion when installed on an Eldar ship; installing them on a human ship would only grant said ship the benefit of its Supreme Manoeuvrability rule, allowing it to perform a Shooting Action in the middle of its Movement Action. The table does clearly indicate "Appropriate Hull Type: Frigate; Power: 50 Generated", so I'm not particularly convinced that this is correct?)

The Munitorium does not correctly increase macrobattery damage by 1.

There is a lot of inconsistency in the use of "Gellar" vs "Geller", "Augur" vs "Auger", and "X-pattern" vs "Y-Pattern" vs "Z Pattern" versus "Q pattern", although this is a problem shared by the original sourcebooks. I can list off the specific corrections here if you want to exactly match the original books, but I think this is a level of nitpicking beyond even my level of pedantry.

Something real weird is going on with certain weapon statistics when modified by other components, resulting in modifiers being applied multiple times when they should not be applied more than once, or even at all. Specific replication steps:

1. Open the program (most recent dev build); the default Carrack-class Transport is fine. 
2. Go to Components, Weapons, Macroweapons, Macrocannon; Mars, Install (leaving it in the default Common Craftsmanship and in the first Dorsal slot.
3. Select Macrocannon; Mars again, choose Good Craftsmanship and +1 Range, and install it in the second Dorsal slot.
   1. Click over to Export Data to confirm- do far everything is correct. Two macrocannons are listed with Range 6 and Range 7.
4. Go back to Components, Upgrades, Turbo-Weapon Batteries, Good Craftsmanship, leaving Target as default ("Macrocannon; Mars : Dorsal - 0", the first [Common-craftsmanship] one). Install Upgrade,
   1. Click over to Export Data and show that both macrocannons' range has increased- they now show Rng: 7 and Rng: 8
5. Go back to Components, select the currently-installed Turbo-Weapon Batteries upgrade, change its craftsmanship to Poor (which should reduce the Range of the affected battery by 1), and click Modify Upgrade. The Upgrades pane will change to show a single poor-craftsmanship upgrade.
   1. Click back to Export Data to see that the macrocannons are now Rng: 7 (should be 5) and Rng: 9 (should be 7).
6. Go back to Components, Upgrades, select the currently-installed Turbo-Weapon Batteries upgrade, and without changing ANYTHING click "Modify Upgrade". The upgrades pane will correctly show one Poor-craftsmanship TWB upgrade as installed.
   1. Click back to Export Data to see that the macrocannons are now Rng: 8 (should still be 5) and Rng: 8 (should still be 7).
7. Go back to Components, Upgrades, select the currently-installed Turbo-Weapon Batteries upgrade, click "Remove Upgrade."
   1. Click back to Export Data and see that the macrocannons are now Rng: 8 (should be 6) and Rng: 10 (should be 7).
8. Go back to Components, Weapons, and uninstall both of the macrocannons. Install two Thunderstrike Macrocannons, the first Good Craftsmanship (selecting +1 Range) and the second Common Craftsmanship.
   1. Click over to Export Data to confirm that they show the correct ranges (Rng: 5 and Rng: 4 respectively).
9. Go back to Components, Weapons, remove the Thunderstrikes, and install two more Mars Macrocannons- the first Poor (selecting -1 Range) and the second Common craftsmanship. There should still be no upgrades installed at all.
   1. Click over to Export Data and see the ranges are now listed as Rng: 8 (the Poor-craftsmanship one, should be Rng:5) and Rng: 7 (common, should be 6).
10. Continue futzing about with various upgrades and watch the numbers get further and further out of whack.