What's weird about a lot of the retcons sprinkled throughout here is that they don't seem to serve a purpose of tying later story threads in better or making things more consistent, but just completely random instead.When Newsarama asked Piskor if this story is meant to be viewed as canon, he said :
"Here’s the thing, as a cartoonist, I really can’t be bothered with that kind of stuff. I’m just trying to tell my story, my definitive X-Men comics. I’m trying to make a graphic novel out of 8,000 pages of periodical storytelling.
If Grand Design is used that way later, I have no control over that, but this is really my love letter to Claremont and crew. I think it’s silly to cry about “canon.” The comics you loved as a kid, they still exist, so don’t worry about it. Let people tell the story the way they want to tell it."
Think of it as a personal interpretation of the X-Men mythology where Piskor is trying to streamline the old continuity and stories that were told between the 60s and the 90s in order to give a clearer picture of the franchise for new fans while also adding new things inspired by other medias making the story feel fresh and entertaining for old fans too.
For example in the first issue you can see Wolverine and Captain America meeting a young Max Eisenhardt, it never happened in the current continuity but it happened in X-Men Evolution, same for Xavier who lost his legs when Cain Marko became the juggernaut while in current continuity he lost them after a battle with Lucifer (the first time at least). Of course not having Colossus defeat Proteus is disappointing ( same as the 90s cartoon where Proteus was "defeated" by Xavier), but who knows maybe Piotr will have his big moment later.
So to answer your question it's just a cool story that the writer wanted to tell, it has no ambition to replace the original continuity it's just a modern take on the franchise influenced by the comics/cartoon/movies and by Piskor own experience as an X-Men reader, that's why I said I was happy he didn't include Deadly Genesis because I can't stand this story. Deadly Genesis, House of M and their consequences are what ruined the X-Men for me.
Of course it's just my opinion and I can understand why other peoples don't like the writing (the retcons especially) or the art so of course for them the story doesn't mean a thing but for me it's just a fun book that reminds me of why I used to like the X-Men a long time ago.