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It would be weird to have Magneto not have that Holocaust connection. I wouldn't be surprised if they take the angle of where his grandparents were victims, so he's always been angry/upset/passionate about that situation and how it tore his family apart and they're in a bad way currently because of it, and now he sees the direct parallels to the current mutant situation, and goes from there. It'd be different, but I think Disney could do it.Sliding timescale
Magneto has to be a Holocaust/WWII victim forever though, no other way to explain his origin.
As for mutants in general, especially since as of yet they don't exit in the MCU (I don't want to see any "they've been among us for decades blah blah blah" neither), I feel like they're either go the route of...1) they're a result of messing with time and space from jumping around in EG as we're thinking, and we start this next phase in a world with mutants (though they won't be acknowledged quite yet); 2) a shock wave, explosion, or something similar happens in EG that activates the gene in people, and eventually they start springing up over time, referencing that event that started it all; or 3) Scarlet Witch is going to be the mother of mutants via something catastrophic she does. I could be wrong, but in the current world that the MCU exists in, these ideas make sense to me as ways to explain the introduction of this new species.