Back after a week-long hiatus... at last.
Anyway - I've made the observation that the ISO tracks of some Saturn games - rather, the ISO9660 filesystems contained in them - actually have pseudo-files pointing to logical block numbers outside the ISO track in them. These are the CDDA files (and you often do see them named as either CDDA*.* or DA*.* or something similar), and the game will expect each audio track to start/end exactly where the corresponding file says it does.
On the other hand, there are the games that simply go by track numbers when playing audio - it doesn't matter where audio tracks start/end, i.e. how long they are, just that the right number of tracks is on the CD and that they can be accessed CD-player-like via track numbers. With those kind of games, you won't find any references to CDDA tracks in the ISO.
So, whether or not the ISO contains file pointers to audio tracks seems to be a good indication as to whether the game will play altered/custom audio tracks OK or not.