Content gets cut from games all the time. The reasons are usually time and resources, nothing nefarious.

Danse's alternate ending was probably cut for continuity reasons, though -at some point, editorial probably realized that it doesn't actually make any sense for an exiled traitor synth and an outsider like yourself to be able to just remove Arthur, the idolized and worshipped last seed of the Maxson line.

Even with the right to challenge being in the books, the way the legend of Maxson has built up among the current ranks as the elder that rebuilt and reunited the east coast Brotherhood, took them out of doing nothing and brought them back to glory etc etc, there's no way anyone in that ship would actually go "oh well yeah, our savior Maxson's been challenged by the traitor synth infiltrator and that one scavver we took in for reasons, so I guess he has to step down now." It's pretty bad writing that overenpowers the protagonist at cost of... making any sense, and at some point they probably realized it and axed the whole thing.

Unfortunately since this possible ending was something Danse's character was probably conceptualized with from the start, nixing that subplot also left him kind of unfinished, like there's supposed to be more to it... but now there isn't. He isn't the worst case, though, as far as feeling unfinished goes -MacCready never goes back to his probably still infant son, Cait's whole subplot is resolved by a gizmo with no substance behind her recovery, Strong has no resolution to his milk of human kindness subplot at all... Danse at least has a good emotional payoff in his personal quest, even if he doesn't move much further than that in the end.