Al, Herman's excellent response gives my reasoning for the clone operation using SuperDuper. Once it's set up, regular incremental backups become so easy that they are actually likely to get done. As well, familiarity with the SD process may encourage a user to adopt a regular backup strategy for the startup disc too.
As for the possibility of confusion between volumes, operator error is always a thrilling possibility. However the volume and its clone are allowed to have, and should have, different names and creation times. Also, on startup, iTunes will open the last iTunes library used. If that's not available, it will ask to be shown, or told to create, another. It's not likely iTunes will inadvertently get confused this way.
As for the possibility of confusion between volumes, operator error is always a thrilling possibility. However the volume and its clone are allowed to have, and should have, different names and creation times. Also, on startup, iTunes will open the last iTunes library used. If that's not available, it will ask to be shown, or told to create, another. It's not likely iTunes will inadvertently get confused this way.