Honestly fungal cave in particular doesn't make much sense. We're getting those people out of the cave to live in the quality of our settlements, gaining their settlement as buildable would really kill the point of the quest. And honestly it would be the same for any situation where we go get someone from somewhere to bring it to our settlements. If we can build a settlement there afterwards, why are we taking this person out to a "better" life.
That being said, I could see the complete opposite of your idea. If they wished to, the SS2 team could make a quest where we go somewhere and meet people who have the place to build but lack ressources/know-how and maybe we can earn their trust (it's a game, there needs to be a mission or stuff to do) until they decide to join us and let us build there. That could work storywise and mechanics wise. I'm not quite sure it's something they want to do as they often said thy don't want to alter too much of the outside world but in the case of an interior cell, another vault? A new section of the subway system? An abandonned giant empty factory? There are quite a few options that would be possible.
But that's even if it's something they want to do. Let's be honest, it's not like they are not already working on enough stuff at the same time. But I could see some possible ways to gain settlements that were created by the team in future chapters, just not the way you described it.