IMO, the story the mcu will be going to use for the mutants was always going to be different than the ones from the comic or even the 2000s movies universe. MCUs secret invasion is also more about the integration of refugees, and everything that comes with that, than an already existing population of people that are just arbitrarily different than the majority of people.

They already changed stories a bit with Hollands Spider-Man and I think it worked nicely.