You know, you could have just made one thread.
Well, anyway, the movie is where things get complicated. There is an unfinished version of the film, back when it contained the plotline from "Deleted Scenes." You can learn more about that version of the film here.
The movie on Disc One, from what I've always understood, is the same as it was in theaters, except that it might be full screen instead of wide screen, but I'm not sure. The movie still has the opening with Mastodon when you press "Play" on Disc One, unlike most DVD releases by Disney Pixar where you have to look at "Bonus Features" to find the short film from before the movie. I never saw the full movie in theaters to be quite honest. There was a time in my life when I wasn't allowed to watch ATHF because of, well, everything. My mom knew better.