Why not take the part of the code that Acidia added where you can choose the equipment for NPCs, even if you don’t yet have the commune up and running, so long as you gained significant trust with the particular NPC (by completing mission(s), giving them lots of valuable items, etc).
This would be good for roleplaying elements too. For example, you could have an NPC companion that could be your character’s spouse and it could be just you and them holed up in a safehouse somewhere. Naturally, with them being family they would be inclined to listen to your suggestion/orders about what clothing and weapons to equip.