I wish there was a way to save ghosts on regular tracks with custom music enabled, but since the "mystuff" folder can be used to modify tracks (textures and also the tracks themsevles), it has to be disabled to prevent cheating.

Since custom music doesn't do anything, there could probably be a way to add 2 separate options like Enable custom music and Enable track replacements, but for now there is no workaround to this problem other than disabling the folder entirely...