An Untitled Story/WMG
DeepTower isn't a tower at all, but a massive tree and is, in fact, analogous to the World Tree.
The lower levels at least have branches and at the very top of the NightWalk side of the tower where you meet the "find the flowers" ghost, there is a green roof, which could suggest a large canopy higher up. It might not be something that would strike players' minds initially, but taking a look at a full map of the game (Warning: spoilers, obviously; also, large image size), it becomes pretty obvious.
However, the WMG doesn't end there: when you explore the area where the roots might be, you find yourself in BlancLand, where the level design takes on a minimalistic quality. My guess here is that at the "roots" of the world, things were created to be at its most basic and as the tree grew and developed, the world began grow as well and become more complex.
Shakespeare the Ninja wrote the diary page in the secret library.
It talks of learning from the spirits and using the energy inside them. He has teleportation powers and seems to glow with energy...
== Shakespeare the Ninja is a transformed bird ==. He can apparently fly, and he knows about both birds and the ghosts...
The game takes place on the edge of a large Floating Continent.
CloudRun, MountSide, BlackCastle and the Bottom aren't at the very bottom per se. They are very high on Earth and the said floating continent is even higher.
- Perhaps Black Castle is on Earth? It's near the bottom of the map. MountSide could also be on Earth, just on a very high mountain. (In fitting with this theory, Cloud Run could be in the sky of Earth, just under the floating continent) How do you explain The Bottom, though? Any idea what it actually is, and why there's a random floor for no reason? That has always perplexed me.
- My guess: The Bottom metaphysically represents the whole of the Bottomless Pit the game's landmasses are floating above. It doesn't exist in a physical sense.