You're kidding me? At least when I chalked it up to not being in HD, I could understand why they did it (once again, not to excuse them for not going the extra mile) but if it is HD, that's just unbelievable to not have the seamless branching at that point.
I'd say that it's almost definitely because the deleted footage was finished on NTSC video so it couldn't be used for a Blu-ray. That doesn't excuse not going back to the footage and making an HD transfer of it but it's probably the reason why there's no extended version on the disc.