The X-gene is not their origin, it's the source of their powers. They can easily change the source of their powers into the brain slot they came up with in IM3. And easy as that, them being mutants is solved. It's honest to god that simple. Them being mutants is NOT an integral part of their characters in the classic Avengers comics, it's just an explanation for their powers.
Their actual origin story can only be told by Marvel, because Marvel owns the rights to the High Evolutionary, the Wundagore mountains, Chthon/The Other, etc. Not that all those elements will be completely used, but if they were to keep it somewhat true to the comics, only Marvel could tell the story of their actual origins. Suffice to say, their origin does not stop at Magneto giving birth to them and actually them not knowing who their rea parents are is an integral part of the characters in the early comics and is meant to represent a theme of family and bond between siblings. Them knowing who their father is completely ruins that and turns them into completely different character conceptually.
So basically, all this about them being mutants and Magneto's children are non-issues that people don't understand because they know of the characters, but don't actually know about them and won't take the time out to research a little about them before going on silly rants like the one in that vid.