Latest Quest ISO, testing on CD32+TF330 again: preloading the music works, it takes 15-20s but the pausing glitch is gone from the title screen and the game. (Besides, plenty of CD32 games take that long to load...) The glitch you mentioned at the end of the track is present - sounds like it's reading off the end of a buffer and interpreting miscellaneous memory contents as audio data?
Latest NoneOfUs ISO - same, although the loop glitch sounds like audio rather than non-audio data in this case :) Maybe just the way stuff ended up ordered in RAM.