Tony, I believe he already has. Add me to the list of those who would really appreciate alpha layer support as a means of telling Photosynth what to ignore in its analysis, if not for presentation value.
In my Buzz Lightyear synth (I'll grant you, the model is very nearly textureless and I also got too many video frames with interlacing artifacts) I got a huge number of hits in the white areas surrounding Buzz due to jpg artifacts. It would have been much appreciated to be able to save a png version of all of the frames with the currently white background portions being painted transparent and saved in a lossless format.
There are a number of things I intend to try next time I try a similar synth which should improve the results, but again, they are a bit of a cheat compared to true alpha transparency.
Lastly, could you explain what happens when I make a copy of my RAW images and instead of converting them to jpg, simply rename the extension? They do synth.