Since there were only a handful of additional changes in '04 and 2011, it would probably be a simple matter of using seamless branching to include them on the same disc as the '97 version. Then the “final” and unaltered versions could each get their own discs.* So, in other words, this would be very similar to the blade runner set.
I think the '97 SE should absolutely be included. It’s what started this whole mess in the first place, so it provides historical context for future viewers. Also, as stated above, it was the first/last time in 20 years the films got a wide re-release in theaters.
*This assumes of course that the 2011 version isn’t already the final version, which we don’t know for sure. Tack said the roadshow screening he went to over the summer looked very different from the lowry master, but was still the 2011 version in terms of content. The 04/11 changes he said looked different from the rest of the movie, suggesting they were simply copy-pasted into the new master. If this version is in fact the final version, I’d still like the '97 version included on its own disc for history’s sake. I would obviously inderstand, though, if the unaltered version was the only other thing included.