Thanks for taking the time to give feedback, and for playing the game!
I have a design philosophy where I want to encourage the player to experiment with the tools they have available. But there are tutorials at the start to explain spirit form and how to use it to interface with the puzzles, interacting with the first set of puzzles in normal form triggers them. If you didn't encounter those then that's a problem I need to solve. I can picture a scenario where the player uses the abilities from the menu before learning the shortcut keys, which would bypass the explanations so I'm making notes on changes to address that.
All the interiors are indeed 3d (using mode 7), but only one is a labyrinth and there's only 1 ostrich in there. The features about it you describe are all intentional to make it uncomfortable, liminal, and a bit spooky. I take inspiration from ps2 era horror for those decisions.