Uhh, I don't know if I like this.
Edit: Thought about it some more.
While the fact that this is a computer program doesn't invalidate everything that has happened it explains away all of the weird elements of the world in a way that I don't find satisfying.
Why don't all of these weird elements seem to make sense? Because it's a computer game so they don't have to.
It doesn't entirely take away from the story and it's not like this was all a dream all along or something, the characters are still living beings with agency and stuff but it's not a very satisfying answer to the central mystery that was built up throughout the story.