Just a thought, and by all means feel free to just ignore me if you don't like the idea.
In the process of the first 'journey' from the Temple of Light to the Temple of Shadows, give Link a useless custom item that modifies his tiles to that of the 'Chaotic form'. Then, in each of the 'Temple of Light' entrance rooms (As in the portal rooms), use a script to remove this item from his possession. And in each of the 'Temple of Shadows' entrance rooms (Again, the portal rooms), use another script to place the item back into his inventory.
This would handle any and all tile modifier problems, and Nick's script can do it perfectly.
And I don't think you should wimp out on this... because it would be cool. But if you decide to go that route, you could create another 'useless' item that actually appears in the inventory, and have the script check for it before adding/removing the 'Chaotic form' item (Which of course would not appear in the inventory, even though it is kept.)
Also, if you add that clause that renders the Sacred Realm/Chaotic form temporary, you could also put in another subtext (That disables A and B, or maybe just the sword.) That way, it forces the player to get the Moon Pearl. And of course, as soon as the player has the moon pearl, the script would go inactive, allowing further progression in the dungeon.
