I think they've already introduced a great way to introduce mutants in Endgame with that energy wave that Rocket detected after Thanos snapped his fingers and then twice more with Banner's and Stark's snaps. The energies of the stones have given people powers before, who knows how many x genes the energy wave activated? Before that, mutants were extremely rare. Maybe a hundred ninety-eight in the entire world, to use a number from the comics.
That's honestly their best route. Merging in a parallel (not the FoX-Men) universe would be far too unwieldy. And having a massive population remaining a secret all this time just strains credibility in the x-treme. This gives them a very good reason as to why they weren't a major presence before while still (via the 198 or whatever small number they go with) easily allowing for any prequels or flashbacks.