I bought the iTunes version and as far as I can tell it downloads the theatrical cut and makes you stream the ultimate edition. Which is frustrating, I can never see myself wanting to watch the theatrical cut ever again.
That kind of sucks. I guess it's a limitation of digital formats. Either that or download two copies.
I wish the movie file itself could contain all the clips, and just branch out as it needed to. Guess it won't make it a universal file then though.