Matt, I think that letting the system automatically determine what is best by default (as both you and the Photosynth team is suggesting) is appropriate, but I do appreciate having a manual override to say, "No, I meant it to be this sort of panorama.".
There are times that I give ICE a set of photos taken with a rotating camera and it falsely detects one of the planar motions that it supports, so it's good to be able to say, "No, try again with a rotating camera motion.".
I think that there's a parallel here.