I may be remembering wrong, but is implied that the mission Jean goes on the start of the game is to check on your university/Farouk trail, the reason her power is messed up being some fuckery of the Shadow King, so unfortunally i think Null wasn't able to seal him, the millenia old mutant still being around to screw around in the world. That said it would be a fun alternative plotline, Farouk being a kind of devil on the MCs shoulder. As things are now i'm guessing Farouk evaded the X-men Team Xavier send with Jean, or just had a mock combat with them to play around, but meanwhile noticed Charles mental locks on Jean's mind and put a small crack in that so see what happens/create a problem to Charles deal with while he disappears for now.
Yeah, even in the show, Legion, is implied Xavier erased his own memory of David to prevent people to find him, meanwhile on X-Men Evolution Charles just didn't know until David called him, while coming out with this theory i had the thought that maybe something would come up on Null exams in the infirmary, then i kinda of dismissed it because Reyes just running a random parternity test on Charles for Null sounded really silly lol So yeah MC being in the foster system and the Family/no Family option just meaning if you were adopted or not kinda of makes sense, since Gabrielle Haller dies when he is young on the comics, if the theory holds this version may died too just not in a super traumatic event that awoke his powers.