> A-Base D-Landing has 'Factory' as a building function, but under that definition I could technically use a Room-level factory to refuel a 1500 tonne rocket
Looks like I need to clarify the entry: a Factory building function (and 3D printer function) only acts like a factory cube for operations at the Complex and larger scale (that's what I mean by factory printer). At smaller scales, it acts like a 3D printer -- at the Room scale a workshop printer, and a freighter printer at the Facility scale, but it allows you to manufacture stuff (like wire and fabric) instead of printing objects.
> I can't seem to find where water tanks would be created on-site
Either using the Refueling rules in the Site Actions chapter, or the Employment subsection under the Migration & Trade section in the Encounters chapter in the Crewed Rules.
This is actually quite a bit more complicated than it looks like and has a lot of abstractions that I really want to write up as an entire "economics of colonies" essay at some point. Essentially, while the crew administers the site, they don't own all the proceeds from it: usually because they're working for a Mission Control, but maybe also because the site has its own independent economic activity. So the amount of water tanks they get from factory refueling because they helped build the factory is actually a reflection of the value of their labour, and not the actual amount of water that the factory can produce. However, for anything that contributes to the site, the "taps open" as it were and the full output of the site can be directed to it. That's why refineries, printers and factory buildings scale up their output as the map scale increases for the purposes of making other buildings, but the amount of water that the crew gets from a factory does not.
> When I zoom into that card, do I still create a structured map via the Crewed Rules
Yes. Whether this is a structured map actually depends on the site population (see the Civil Maps chapter of A Facility with Words) but for the purposes of zooming into a card this doesn't matter that much and I still don't think I have the way this works right in AFwW. The idea with a structure map is it is sometimes the interesting "slice" of a larger map and so is the default map type for many things, instead of being a complete map of the site at that scale.
For aerostats, I would recommend creating a floor plan when you zoom in rather than a structured map as floor plans should be symmetric. I should probably write that down somewhere in the rules...
Mixing maps that you create and build is going to be supported better in the next update of (A)-Base (D)-Landing, where you'll have the ability to infiltrate existing colonies. But generally once you've placed a card, you shouldn't really have to zoom into it to build on the zoomed in card as far as I can tell, because you've done the hard work of printing it, and upgrading it should be easier than trying to zoom in to do the same. I had thought I'd said that you can't build beyond the edges of the map but it looks like I missed that.
> The mission plan list in This Space Intentionally confuses me a little bit
It is only intended for year long turns. At smaller scales, spacecraft are essentially stationary on the HF map for the entire turn length -- although they will move if you get into trouble (and have to resolve a year long turn as a result) but only once per year. I'll have to clarify that. Operations are also year long and will "resolve" with trouble, but also that could be potentially be abusable in ways I haven't thought of. I've experimented with ways of subdividing operations and events into month long turns, and it plays ok but just adds complexity for not much pay off.
Hope that all helps and apologies for missing this.