DVDs have had Seamless Branching Technology integrated into them for a long, long time now...look at James Cameron. Almost each one of his films has incorporated Seamless Branching in order to offer both the theatrical and Director's Cuts of his films (The Abyss, Terminator 2, Aliens). Fox has proved that they are masters of the technology.
How about putting the original, remastered Theatrical Versions as well as the new DVD cuts onto dvd using Seamless Branching? That way, you simply choose what you want to see at the initial menu, and it all plays smoothly. This way, you only have to put the ADDITIONAL footage on the disc rather than 2 full movies.