What you're talking about is seamless branching, and when you have a few scenes that are cleanly inserted without music changes, as is the case with T2, seamless branching is an excellent approach. Unfortunately, there are so many small edits in the SEs that it makes seamless branching a big undertaking.

My ultimate box set would be separate 3-disc versions of each film, with one disc containing the original cut, one disc containing the final Special Edition cut, and the final disc containing all the special features. This would allow maximum bitrate for the best A/V quality and keep the presentation very clean. It would also allow them to break up the set into indivdual 2-disc releases very easily, like a 2-disc original cut and a 2-disc Special Edition.