I'm not going to bother with 1 or 2 because I don't particularly care. Let's see...

3: Those tiles used to be occupied by the Lagunicus tileset, and still have their mask. When Lagunicus was made into a separate planet, tiles from Exoticus were just randomly (and incompletely) pasted over the old stuff.
4: The gem you're waiting for people to name is the blinking red gem, right?