In theory, song ID is supposed to be used during the library synchronization as the first thing that is checked. That's probably working as intended for merging your songs together. When it comes to merging the setlists, I'm guessing there is an issue in the code where it's just looking for songs by title right now and using the first one that is found. I will see if I can improve that logic to use song ID first like the rest of the synchronization. So you can hold off on renaming your files.
Mike
Mike