Likely because there is an expectation for them to exist in some capacity aswell, since in the end they are still a definitive Marvel IP.
It's a "between a rock and a hard place" situation.
The mutants/X-men are attention hogs and would logicaly dominate the entire discourse around super humans in any new version of the Marvel Universe they exist in.
The main universe can arguably only largely avoid this because of how much it's rooted in the "simpler times" comics of 60+ years ago where such concerns did not exist in favor of just having enjoyable mostly self contained "one issue/one story" adventures.
Essentialy any time the above mentioned questions would be asked someone can point at the original comics and claim "because it has always been this way".
But a new Marvel universe, which is following more up to date standards of continuity and world building would risk being quickly smothered by it their presence and importance. As happend with the original Ultimate Universe and how Magneto's actions couldn't be simply swept under the rug, but his world conquering/changing plans are an essentialy part of the X-men mythos. Even without Ultimatum there would have likely been a breaking point for how much one or the other could remain the more important focus.
However the mutants/X-men are also a high profile Marvel property and essentialy part of the classic Marvel Universe. So their absence would be glaring aswell.
So this might be their compromise. Have X-men and mutants, but keep them small and contained as long as possible (which given the track record of comics these days might not be for long regardless of how well New Ultimate Spiderman was received), so that they can properly re-introduce all the various non-mutant versions of super humans/villains/heros first.