OP goes in quite a lot of detail as to what changes, but do note it goes a bit into spoiler territory, specially since the stories exist in a continuum.

It does make me curious though, how the changes do pile up, both being 70+ hours-long games with a ton of story. Welp, guess I'll have to finish these games a 5th, 6th and 7th time to be sure. Such a tragedy. /s Also saw no mentions of it, but Mary Skelter 2 has as an unlockable the first game, Mary Skelter Nightmares, so I'm also curious if the changes affect it too.