Just based on casually looking at randomize_music.js, it seems that each area/boss has its own setting for what music to play, so it seems like it would be possible to alter the code so that each area/boss has a unique music selection, rather than 50% of the reverse castle playing the same song like vanilla. If you want to ensure that each piece is played at least once, you could make an array for all the areas/bosses, fill it with one of each song, fill the remaining slots with randomly selected music, then shuffle the array and assign the music. I would try it myself, but I'm not too good with JS, and some of the addresses aren't labeled currently.
Just based on casually looking at randomize_music.js, it seems that each area/boss has its own setting for what music to play, so it seems like it would be possible to alter the code so that each area/boss has a unique music selection, rather than 50% of the reverse castle playing the same song like vanilla. If you want to ensure that each piece is played at least once, you could make an array for all the areas/bosses, fill it with one of each song, fill the remaining slots with randomly selected music, then shuffle the array and assign the music. I would try it myself, but I'm not too good with JS, and some of the addresses aren't labeled currently.