It would only be practical for movies where only a few scenes are "altered." You can't have a lot of alternate scenes going on. So Star Wars is out of the question.
For a movie that's a "director's cut," though, it's quite easy to place your chapter marks and provide an optional short version which skips certain chapters, and slaps on one or two alternate scenes, say, an alternate ending. Alternate endings are pretty easy to provide, as they start on the same frame as the other ending.