X-Men does not make sense in a unified Marvel Universe. X-Men is a big broken aesop about how it’s wrong to discriminate, and mutant civil rights are conflated with minority civil rights (or, even worse, gay civil rights) as part of a big meta-narrative argument for why it’s wrong to fear people who are different. There are two major ways in which this falls apart. You can’t equate mutants with blacks or hispanics or whatever, because most blacks and hispanics don’t have the inborn ability melt a city block with the snap of their fingers. People aren’t scared of mutants because they’re different, they’re scared of mutants because they go flying zapping things with energy beams. People of different colors are more or less the same, y’know, we think, we feel, we have families, we do not have super powers.
Secondly, what is with people being okay with people who mutated after they were born to get super powers? It’s this second point that makes the unified Marvel Universe kind of stupid. Mutants are born with super powers. Sometimes these powers are dangerous, sometimes they’re lame. Regardless of their powers, everyone is all “Oh, noes, the mutants! I’m scared that my suburban living will be disrupted by their existence!” Never mind the fact that it usually is. (“Well, if there weren’t mutants running around, maybe mutants wouldn’t have blown up the _______!” The strawmen have a point.) But enter the Fantastic Four or Spiderman or some other guy who got his powers in a radioactive accident (hey, don’t those cause mutations?), everyone is all “Oh, they’re so great! They’re wonderful! Scientists, philanthrophists, blah blah blah!” Never mind that they’re for all intents and purposes exactly the same as people who are born with their powers.
So, yeah, it makes no sense to have a world where everyone hates people with super powers, except if they were not born with them.