Overriding ModPlugSettings didn’t work for me either. Nor did changing the settings internally and re-compiling as per these instructions.
This looping behaviour is the whole point of MOD files, they were pretty much invented for video games. You have the intro of the song, then the main part of the song, and then it loops back to a neat loop point in the song some time after the intro.
Ignoring the looping by default is only useful for media player type software, and that’s it. It completely breaks their intended functionality for games. A function to enable/disable it would be best…