Also songs with noticeable differences:
Knuckles Encounter (Cutscene): Extra/different beat before the loop
Mushroom Hill (Aquatic Relix 1): No echo on the main Lead, no harmonics added in some parts and different loop
Slot Machine Theme (Cosmic Casino Act 2): Lacks the intro, different stereo setup, different volumes, different backing harmony and completely different percussion
Other songs may also have differences but I couldn't point the out just by listening (just maybe some panning/volume changes). I intend to record wavs of the prototype tracks and try 'wave cancelling' with the final songs.