I thought that they could branch on Blu-Ray and provide all three versions of the film on a single disk?
They can. Close Encounters of the Third Kind and Blade Runner both branch three versions on one disc. However, in the case of the Director's Edition, Paramount is either a.) unwilling to shell out the money needed to uprez the DE effects to 1080p resolution for Blu-Ray.... or b.) is waiting to double-dip later on.
Now what Paramount can do is branch the theatrical version and the TV version on one disc but they'll probably put the extended TV scenes in a separate section.
Well, not entirely. Seamless branching relies on the movie being pretty much identical from one version to the next. If there isn't a lot of overlap, it isn't worth doing. So while they could do seamless branching for the theatrical version and the extended version (since the only difference is the presence or absence of those few scenes), it'd be much more difficult to do so with the DE, considering the number of trims, rearranged shots, new visual effects and, most challengingly, the almost entirely new audio mix. There's just nothing left that's 100% identical to the theatrical version. So they could do what Blade Runner did, with the DE being on one disc and the two prior versions being branched on another, but they couldn't put all three on the same disc.
I'm interested to find out what kind of features the disc will have. Will they recycle the same self-congratulatory featurettes from the original DVD or will we get something a little better?
As I recall, the reason the DE was delayed from the beginning of 2001 to the end of 2001 was that all the special features had to be redone, since they weren't masturbatory enough and needed to be whitewashed. So I doubt it.