I happened to be randomly looking around the CBM site and found an article "X-Men: Ten things that need to be done/answered" (horribly paraphrased, I'm sure). One of the points said now that the X-Men, and mutants in general, are back under the Marvel umbrella how do you explain where they were?
Well, what if they weren't there at all?
What if the answer lies in the events of Avengers: Endgame - the infamous "Blip"?
Now follow my logic - we are assuming that mutants didn't exist in the timeline pre-"Snap". That would easily explain why they haven't shown up in the years prior or during the 5 year period between the two events - they don't even exist yet. When "the Blip" brings the missing back, that event could be what actually triggers the mutant gene. Something like the mutant gene already existed in select people but was only activated when they came back. This would now bring mutant-kind into the MCU, and a world-wide event like this would explain away why there were none before but many now. Smarter minds than I could explain exactly how this happened - wherever the missing were stored in that 5 year period nurtured the latent gene to activity, just because, etc..
Straightforward and easy. Marvel doesn't have to come up with some convoluted bs trying to explain that mutants were in hiding, or were formed by Ego, or a sneeze from Galactus dropped mutant-gene ridden snot into our atmosphere.
Again, just a theory but I think myself a good one. Disney/Marvel, if you're reading this its my idea, dammit. I only want 2% of world-wide profits for the next release and its yours.
Happy trails,
Lloyd