I've managed to stay away from a lot of "big" spoilers so far, so I could be way off base here, but it doesn't seem to me like there is going to be a section of the film that would require a lot of "temp track" stuff. The main reason that the score in TPM was destroyed was because of editing four different stories at once, and in AOTC the score was destroyed before it started because of all the unfinished special effects and anamatics. Oh, and Ben Burtt's turnip farts, which I can't forget.
The way it seems, the last reel of the film is going to be pretty much Anakin versus Obi-Wan and Sidious versus Yoda as far as action goes, and I would imagine that while there would be some interplay early on, the last few minutes of that section of the film would more than likely be just Anakin versus Obi-Wan due to the emotional nature of it all. I could be wrong, but is there really a whole lot that could require extensive re-editing (and/or turnip farts)? Then we'll have the end of the film which should be all subdued types of cues, what with births, deaths, rebirths, etc., and I can't think of a reason why none of those scenes haven't been completed and organized to a point that would require the score to be obliterated.
The reusing of the Main Title bothers me though. As I don't have Hyperspace (I will not pay for content, pornography or otherwise), I don't know if this was a JW decision to reuse an old Main Title cue, or if it was a Lucas mandate. Or if Ben Burtt wanted to highlight this really cool tractor backfiring due to a potato in the exhaust pipe and the Main Title was judged to be unimportant.
On an only semi-related note, I'm really hoping that we get full unmolested versions of the prequel scores on double-CD sets (along the lines of the RCA SE soundtracks that Sony recently reissued) at some point once all this is done. Even if there is no music scoring the Clone War in AOTC, I'd still love to have the pieces that didn't wind up on the single CD soundtrack.