Whenever I read such articles as this, that promise to have a list, or tally. I try, first, to play a little game: I try to guess the subjects, in this case films, of the list or tally. I guessed a fair amount here, but not all, but you omitted only one film I guessed at... Touch of Evil, which was initially butchered by the studio in much the same way The Magnificent Ambersons was... But thanks, perhaps to the experience of Ambersons, Touch of Evil was able to be restored with the help of long memo Orson Welles composed at about the time of the release of the butchered version and about his intent with the original.
The Godfather III/The Godfather Coda: Death of Michael Corleone are, in fact, both fine films. I think I slightly prefer the newer one. They suffer only in comparison to the truly great films that preceded it in the trilogy. I think, too, that it might be one of Andy Garcia's finest performances. Am I disappointed that it's not as good as the first two? Yes. Does that make it a bad movie? No.
I quite enjoyed both versions of The Abyss and, like you, wondered why it didn't do better at the box office.
I would have led this list with Kingdom of Heaven, as that is the film where the extended cut most differs from its original release. Indeed, I'm tempted to call it a completely different movie.
I was pleasantly surprised to see that I've seen the bulk of the movies listed, original and their re-cut releases. Of your list, I've seen the original Saturday Night Fever, but never felt invested enough to see the extended version. I've never seen La Belle Noiseuse, the Excorcist or the extended LOTR. I will search out La Belle Noiseuse to watch, upon your recommendation. I don't like horror films so won't bother with that one. The less said about Peter Jacksons corruption the better.