Pietro and Wanda could be retconned to have been the first mutants we've seen on-screen. Hydra may have known about the hypothesized "X-Gene" and forced a transformation/trigger using an Infinity stone. Charles is/has beem where he was before the events of the first X-Men issue
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Travelling the world.
Ditto for Erik who was basically hunting Nazis down.
Wolverine is with Alpha Flight and Mystique and Irene are fostering a young runaway Rogue.
Storm is in Kenya, isolated from the rest of the world.
Moira is on Muir Island etc
The basic guidelines for the mutant phenomenon have been laid out in the MCU and the comics already have a clear explanation for where everybody is/has been all this time. The problem only arises when/if Marvel tries to retcon in the entire 56 year history of the X-Men's lore into the MCU instead of naturally building the world in the first X-Men film.