First is it really all connected? If so what Agents of S.H.I.E.L.D. has done with the Inhuman story leaves little room for any unique mutant X-Men social commentary. Because in the MCU not the comic books the Inhumans came first and the discrimination, the government and non governmental agents and vigilantes chasing the Inhumans down to kill or turn into weapons has already been done. The mutants would be just another group of 084s facing the same as the human results of Kree experimentation. About the only case to be made is that Inhumans can refuse terragenesis by maintaining a strict diet, assuming they know that they are Inhuman.
Given the press conferences by US President Ellis, in the MCU and news media coverage we should be at the point in the MCU where anyone with a power set emerging should be thought of as Inhuman first with nobody asking about an origin story. Best played in Civil War when Tony Stark just blew off Peter Parkers offer of the story. All in the MCU expect to hear I woke up out of this black cocoon able to do this stuff.
Where were the mutants before now? I like the theory that there were few of them and they were on the index like Scorch in Agents of S.H.I.E.L.D. season 1. So why get them into the movies? Because RDJ and Chris Evans have to retire sooner or later so you have some new characters in reserve for that day. I can argue that Brie Larson works as Captain Marvel because you are not casting just for today, you are casting for 10 or 15 years from now. In that vein the famous X-Men characters could be 7 year olds today ready to enter a school when Marvel/Disney pulls them out of reserve for phase X of the MCU. Why 7 now? In my proposal environmental damage from the Battle of New York instead of nuclear experimentation causes the explosion in the number of mutants.
To the question of Magneto. The Shoah due to the pride the Nazis had in recording what they did leaves us with no need to explain to the audience no matter how poorly educated what is going on. We cant freeze someone else in ice and what does an extended life span has to do with his power set. I propose aliens. Even before the Battle of New York the Asgardians, Kree and Ravagers taking Peter Quill at the very least. And recently the Hulk got off planet. Somehow, perhaps the theory of relativity for a short time from the aliens holding Magneto can bring him in young enough for our story when he returns to an earth with others like him.