Art/Design: Not my cup of tea... loud and not particularly thematic. You could reskin the whole thing and not really lose much of the character of the module. The straight cut corners - these are basically a rite of passage for anyone who hasn't had a graphic design education (myself included). We've all been there, but the next step is to use them for purpose, supplement them with added details or deliberately to conjure up a particular aesthetic - like with the "What Really Happened" section - that usage looks cool!

It took me a while to figure out whether the map was vertical or horizontal.

Logic: The Warden kinda needs to piece things together from various places, having a tighter overview and introducing concepts as you go would improve digestibility. 

"Can be found" I'm guilty of this one, too, but I keep seeing it this week. One lesson I'm taking from the jam is to just say "There is" or "X is" instead of using this kind of construction. 

Art: It's not boring, but unfortunately, the way the colors are being used is distracting. Like a number of other people, you've added bright red to the jam palette, which clashes with those other colors. In particular, it's a design no-no to put red text on a blue background — the human eye has a hard time focusing on the boundary between a saturated blue and red, which creates a "vibrating" effect for those Null Protocol mentions. The orange-on-blue in the interior isn't as bad, but is pretty low contrast... the light blue on dark blue with yellow for the accent text is a good choice, like you did on the outside.

Writing: I like the concept, and the endgame is a pleasant surprise, in that with a living cave you just kind of assume it's going to eat the players, so to have the threat be something else is nice. There's a lot that's not really explained, which is common and considered okay in Mothership... however, the one omission I think really needs to be corrected is that there's no physical description of the Harvesters. I can picture a tendril just based on the name, but all you've given me for the Harvesters is that they can move around and that they have snippers. But are they crawling or flying? Humanoid, insectoid, robots? Given that they're the main threat during the escape sequence, they deserve a more thorough treatment than the other creatures.

Game Design: You identified the problem yourself, which is that a reasonable group of characters might decide not to go all the way to the bottom of a cave that's clearly a giant monster's stomach, and then mess with the alien artifact at the bottom. That isn't "risk-averse," that's just reasonable roleplaying. This is usually going to be the problem if designing a scenario with a particular climax in mind that requires the players to do something to trigger it. You can solve this either by having a nonlinear scenario that can be solved multiple ways, or by having the plot driven by forces beyond the players' control and let them just react to it... but if you require the players to be instrumental in doing specific things to allow you to tell a particular story, you're inevitably going to be railroading them.

Theme: It's ancient mythology, and it's Mothership, and it's the shared setting, and you let the players piece together the myth in-game as they proceed. Full marks for this.

Layout: Alongside the color issue, the use of tightly-spaced all caps makes the bottom part of panel 2 (warden notes and engravings) really hard on the eyes. The map is a bit confusing in that I can't tell whether it's meant to depict a vertical descent down into the cave/monster, or is a standard top-down map showing horizontal configuration. Aside from those details, though, the layout and sequence of information makes sense.

Utility: Aside from confusion about the map and the Harvesters, I think this is good to go, and I could easily just take my best guess at those things. The potential need for railroading is the bigger problem and I would probably end up trying to rethink the plot a bit to make that less likely. Issue could be avoided if you just had a really cooperative group of players who will go with the flow because they want to let you tell your story, but not all groups are like that.

Favorability: There's some cute stuff here, but I'm not that into science-fantasy and definitely not into plots that require coercing the players, so I'm kind of lukewarm. 

I like a lot of the ideas in here, I think the aesthetic is fun, and the general setup of "walk in quiet, shit hits the fan, weird horror carnage" rocks! The engravings are creepy and well-written, and I think the Function is a very fun concept to be shaped into a mythologically-known concept! I really dig the cover panel as well - I think the title treatment has The Sauce.

Some scattered additional thoughts:

• Text feels pretty cramped to me across the board. An edit pass to size some paragraphs down and give the text frames some breathing room could go a long ways! I'd also recommend switching the body text font on the outside-left panel to the one you got in the rest, and brighten up the body text on the inside to full white.
• I like the room descriptions - they're seeping some good horror flavor! I would love to see some areas of the map, in particular the Lungs and the Prisoner itself, match up a bit more closely with the descriptions.
• I really like all of the creatures described! I would highly recommend unifying the damage dice to d5s/d10s/d100s, since that's sort of the common MoSh style, but their behaviours and the threat they can pose are very effective.

Overall - really excellent foundation! My aesthetic/layout quibbles are supremely fixable and I think the core narrative here is weird, trippy, and very thematic. I'd have a ton of fun playing in or running this trifold, no doubt.