I'm talking about the mutant population in general. X-Men got plenty excuses why they weren't around. Not all the world's other mutants.Maybe rather than Magneto being WW2 holocaust victim you could do a post WW2 or late 70's rebirth of a Nazi group (or Hydra faction) that killed his family and in the 90's or 2000's he met Charles....
Wolverine you could do flashbacks with Cap in WW2 and he could have been on some in Canada when Thanos came into town cause it wasn't his beef. Lots of ways to work around it.
Edit: Magneto my favorite character so any changes to him gonna make me feel some kinda way regardless, I'll be alright though