@H Gregg, it seems like you are asking for two totally unrelated scenes to be in the same synth. Is that right? Essentially wrapping photos for two (or more) synths into a single one?
With Photosynth 1 (the desktop application) you could upload unrelated scenes together in a single synth and, once online, use the period + comma keys to move through the photos in filename order (which would take you from the end of one sequence to the beginning of the next).
Photosynth 1 also already has support for 'Highlights' (the thumbnails on the right hand side of some synths + panos) which will take you from your current position in the synth to the portion of the photo specified in the selected highlight. In a synth where all photos are connected, an automated path through intermediary photos would quickly be calculated and followed to the highlight. In synths with unconnected photos you would transition immediately to the highlighted photo unless you were in its cluster.