Seamless branching might not fit on the disc without decreasing quality. It's 20 minutes longer than the movie, and based on the IMAX alternating ratio that was decided against (possibly to reproduce what most people saw at the cinema, rather than the relatively low number who saw the IMAX release).
It should also be pointed out that it was likely made at 720p.
I'm not an expert, but many other Blurays are able to hold more than the 2.5 hours on this STID release. According to a quick google search, standard Bluray can hold over 8 hours of HD video, so I doubt expanded the release to 3 hours to include the commentary (or even 4-4.5 hours to include all of the special features
) would be much of a problem. And hey, if it is an issue, release a 2-disc BR edition like almost every other high profile movie does...