They made absolutley sure that NO alterations were made, and that the flims were exactly as seen in theatres in 1985, '89, and '90. (With one exception in Part II: the Part III trailer is still present, however the "Coming summer 1990" is gone.)
There was a quote on the commentary where Gale, when asked, said that he didn't understand directors going back and changing their flims. He said if they did that to BTTF, "That's not Back to the Future!" So things they very well could have gone back and fixed (like wires holding actors and stuff) were left alone for the sake of presenting them exactly the way they originally were.
The "To Be Continued ---->" title card at the end of the first Back to the Future was added for the home video release, because they didn't intend on making a sequel when they released it in theatres. So the DVD does not have this title card.
The end of Back to the Future II even has the teaser trailer for Part III as shown in theatres, even though I personally wouldn't mind it if they would have removed it. Kind of ruins it for a first-time watcher of the DVD set. (No problem, I just made my own DVDr with the trailer snipped out.)
I respect them a lot, and it's a sharp contrast to George Lucas.