I mean, didn't Krakoa more or less accomplish that as well? The difference being mutants decided they no longer cared about being accepted so they completed their mission by creating their own world safe from "flatscans" like the Richards?
X-Men Factor Forever was a favorite of mine and one of the best portrayals of Jott. It came out right in the middle of the dark age and was a much needed break for starved Jean fans or Jott fans in general. This is exactly what hack writers like Morrison, Fraction, and Hickman never understood about the X-Men.
The problem I have with using the Phoenix to solve the world's problems is exactly what you said that in a comic book world with shared continuity, stuff like this cannot last and will never work. It's the same reason why Reed Richards has never used his intellect to solve all the world's problems in one week even though he probably could. I think it's better to not even attempt something like this because it just pokes holes into everything. This will sound controversial, but I never understood why everyone was so fixated on mutantkind's extinction from M-Day. Maybe because it had gotten old fast since that's all the X-Books focused on during this period but I never got why it was considered so horrific that there would be no more mutants. And after years of hearing this being cried about, I was about to jump on the bandwagon that mutants really should die out to spare us from more of this horror. I was Team Wolverine because it was back to basics, reopening the school, where the X-Men should have been all along. It featured all the classic characters and none of these villains masquerading as heroes. I remember the reactions on here and it was a breath of fresh air for those of us who were sick of Utopia. What I'm hoping will happen again now that this current mutant supremacist regime is collapsing once and for all. Xavier's character assassination is another thing I couldn't stand. It felt like a sick joke to see how much worse they could make his character with retcon after retcon. Another reason I despised this era was because it seemed like the era of retcons, not just for Xavier, but in general. Most of which have been completely ignored since then.
In a way, I think Storm and Logan's capabilities as leaders (moreso Storm than Logan because classically in Claremont's run, he refused to lead and delegated that duty to just about anyone else) is precisely because their lives are about more than mutantkind. They are enriched for having more in their world and they bring those experiences and connections to their roles as leaders. Storm is one of the most empathetic and loyal of the X-Men for precisely that reason. And I'll say that before the 2000s, Cyclops was like that too. It's true that he had less than Storm and Logan, but we saw periods in his life where he was ready to leave it all. Like the scan I posted before where he told Xavier to buzz off, the X-Men can handle themselves, he's sticking with Jean in the hospital. Then again during the 90s when Scott was injured after OZT and he and Jean retired. He seemed happy there too. Even in X-Men Forever, he seemed quite content leaving the X-Men for Alaska with his grandparents, father, and son. He learned to appreciate a quiet family life, even if it wasn't possible to have it 24/7 but now some fans think that's OOC because they're used to the dark age where he had nothing else in his life and characterize that as the real Cyclops. Having nothing else in the world should not be a badge of honor. It's supposed to be a tragedy as this panel indicates.