Yeah, having it halfway included is kinda iffy, either go all in (and let the player continuously upgrade their stuff as they gain access to resources) or take it out entirely. I think that you could probably balance it a bit better if you went harder in the direction of taking them into account, though - if having a better extractor design slows down development of settlements, for example, because they have to pay for the more expensive extractors, that's a meaningful tradeoff. It also makes hubs even more of a boost for bootstrapping new settlements, which is neat.