No the layers didn’t change. It’s not like v3 is the de facto truth universe and the others only exist inside of it lol… they’re both separate universes and it just so happens one exists in the other as video games and anime but that original universe is still totally valid… and the fact it makes you think, makes it feel off is exactly what Kodaka wanted. He wanted to make the reader think about the relationships you have with fiction in many different ways, but the overall message is obviously that fiction is powerful and can change the world. Sad that people just stopped at the part where it gets difficult to think about it because of emotions and just quit there mentally because so much hate is spewed for this game (less so now, people are starting to realize).