For the most part, the Base Construction rules seem to be functional. I'd have to spend some time plotting a basic base out to see how they work, but they seem solid.
I do wonder if there should there be a section for the refugees/NPCS that will inevitably come to live under the PC's protection? I feel like we're missing a section on people other than the PCs taking on jobs, handling the base while the PCs are out doing things. Probably some Command and Persuasion rolls to orchestrate things/keep the peace and some general Stamina/Tech rolls for the main Builder/Mechanic having their underlings handling basic tasks?
Maybe something like for any given week, a Command and Persuasion roll can be made. Success allows X number of NPC Inhabitants (not sure on the right amount.... maybe 20% to keep things from being tied to a specific number) to be organized enough manage a Facility's task from the following list: Basic Upkeep, Cow Pen, Cropland, Pigsty, Lookout (maybe grants a passive check on enemy approach?), and maybe Still (allow for both the gathering of materials and production for 1/2 of the still's maximum output per shift?).
Allow for more than one PC to make these rolls, but each roll represents an additional 20% of the available work force put to work. Failure on the Command roll means things don't get done and on the Persuasion roll means that there's discontent growing in the population. Also add some text about building a new facility, having a feast, or bringing back a big score of materials would reduce discontent and that discontent left to simmer may result in a revolt.
If the PCs leave the Base in the hands of the NPCs, a Command roll is made before leaving (with penalties for discontent). Failure means when they return there's been some kind of mishap while they were gone (damage to facilities, lost/stolen materials, desertion/kidnapping of 10% of the population, etc.). Success means that no additional work gets done, but the Basic Upkeep for all parts of the base continue.
It's a lot, I know, but I think it's definitely a part of the base building that should be addressed.