Looking in hindsight, I think Marvel not having the X-Men rights can potentially make mutants feel better integrated in the MCU whenever the X-Men rights revert. It never made much sense for mutants to be feared in a world full of superheroes. But if you already have teams like the Avengers established which have an ongoing track record of saving the world, having that stay consistent when mutants emerge might make their integration feel far more natural.
It would also make sense thematically. Mutants are the next step in human evolution, so why wouldn't they show up after people started obtaining powers?
It would also make sense thematically. Mutants are the next step in human evolution, so why wouldn't they show up after people started obtaining powers?