Some of those downfalls are bugs or just not written as well as they could have been, IMO. There is no reason why the followers fall apart because you alone took over. That one always kinda felt like the bug in 2 with resolving the issue between Gecko and Vault City. Even if you do it perfectly, the ending cards don't reflect it properly.

I had a helluva time getting what I felt is the best outcome with the Khan's, too, because of weird script/logic bullshittery. So when it just doesn't work mechanically, I just overwrite it with my headcanon intentions. lol