Jon,
This might be a daft question but...
What if the difference between 'Upload' (via FTP) and 'FTP Photos as...'? They both seem to do the exact same thing.
Not sure where you're seeing the "(via FTP)" part, but Upload brings up the Upload dialog with the last template you selected. And "FTP Photos as..." brings up the Upload dialog with the FTP template selected. If you only ever use the FTP template then there is no effective difference between the two menu commands.
I'm hoping you tell me they can be set to different snapshots?
Only one snapshot per template can be active at once.
-Kirk