Perhaps I should clarify my original questions.
I'm not so much talking about syncing up in terms of story, but merely in terms of looking/sounding of a whole with the OOT.
But this kind of leads me to my other question: does it really matter? Does the fact that some of the environments in the PT are cg whereas even the most fantastical locales of the OOT (like Bespin) are still "analog" actually matter?
In a world without the SE, would it matter that the PT is as cg-filled as it is?