Well, unused in the sense you can't explore them normally. They're used for cutscenes. What's neat is that they are fully compatible with the 3D flip ability despite never being seen in 3D in normal gameplay. Loaded in Dolphin using methods discovered by aldelaro5.
The locations from Thousand Year Door have a lot of leftovers from that game. In Bowser's Castle, when flipped to 3D the flat Bowser statues have 3D collision, leftover from when they were 3D in TTYD. You can also see a Bowser painting when flipped that is otherwise only seen in TTYD. The ceiling of Bowser's castle has no collision, though the ceiling above the altar in the chapel does.
Mario's house exterior was clearly not meant to be seen in 3D, even though the entire house model from TTYD is present. The ground texture is completely wrong and most of the house has no collision. You can't enter the house from the outside since there are no loading zones, nor can you exit the house when inside. The only way out is to use the Return Pipe.
However as shown in the video, the door in the chapel leads to the final boss room, which is empty after you beat the game. I do not know what happens if you enter the room from the chapel before beating the game, but presumably Mario will walk to the correct position for the cutscene to play, like he does when skipping the Floro Cragnien area to fight O'Cabbage slightly early (using a Thudley jump). Or maybe spawning in the chapel before the final boss triggers the Bounding through Time scene. I honestly don't know.
![](https://s2.save4k.ru/pic/3qP0NbyuMKY/maxresdefault.jpg)