Turns out there is a custom exit for all act 2s in Mystic Realm no matter what. The custom exit uses the floor height to determine which map to go to.
Hence, say you're in map01 and the normal next level you want is map02, and the hidden level you want to go to if they activate something is map03. Set up a custom exit with a floor height of 2, and have the trigger that causes the map change activate a linedef executor to set the floor height in the custom exit sector to 3. Note that the nextlevel in the level header will not apply in single player at all when you do this; however, it will apply in Race, which is how Mystic Realm has a completely different map rotation in Race mode than in Single Player.