You don't need to put a spoiler tag for this. Kevin Feige publicly revealed this before the movie came out that Charlie Cox was coming back. Not to mention the Netflix shows were always a part of the 616 MCU.
Don't think Marvel is interested in telling those types of stories with the X-Men.You are overly complicating something that isnt that complicated. The only thing that seperates mutants from other superbeings is their origin of powers. With numbers relatively low, there just hasnt been enough research done to discover and define what an X-gene is. That could be a new phenomenon that is found and made public just like it was in many X-men origin stories