As usual Nathanael, you've taken the bull by the horns; here, by both informing to such an extreme level (a typical move by you) and also in your testing and explaining of methodology.
I feel your pain about that 1,600+ photo synth using the "Crop Approach" to improve and perfect synthiness. My sense is such an experiment should almost assuredly work wonders, once you find the correct number of photos that will allow it to process without failure. The low limit on the number of photos that actually work in the Photosynth synther is the second most frustrating aspect of Photosynth for me. (The fact that the problem occurs after hours and hours of processing most of the time is first, and the incorrect aspect ratio of the thumbnails as third, probably)
Anyways, impressive work, Nathanael!