Some of these require you to play on VS mode, editing the rules and items of the match will NOT prevent you from unlocking the stage.

Stage	How to unlock
Ascension	After unlocking all 3 stages, from the Main Menu, select Archives, and then change the page to Ascension, and enter the following code: right, up, left, right, right, down, down, up, down.
Moonstone	After playing every non-unlockable stage at least once, play the Sacred Ground stage on VS until you unlock.
Sunken City	Play VS mode, once selecting a stage to play on, select Random. Must do this a few times first to get it to randomly select the hidden stage.
Towerforge	Unlocked after completing the King's Court stage in Quest Mode on any difficulty.