The locked doors always appear at the same Y position even though the game doesn't classify them as fixed-Y objects. I know the editor makes it seem like you can put the locked doors as high or low as you want, but that's only because it's the way the game stores it internally. It ignores the y position you want and just puts it at the predetermined height. (unfortunately)
As for the hidden town and hidden palace, it's kind of weird. Sorry about that. Here are the steps (It's a bit of a process):
Modifying the Hidden Areas
In East Hyrule, right-click on any other area and choose Seek Index.
Type 49 for New Kasuto or 53 for the hidden palace and click OK. The index you typed should then be displayed in the top pane.
Press B to access a very low-level binary encoding of the area's properties. Bits 2 to 8 (inclusive, counting from 1, from left to right) encode the y position. Notice that it's zero. This is how the game hides the area. change it to any seven bit value of at least thirty and then save. (Thirty is the minim y coordinate on the map. Lower than that goes out of bounds.)
To help you out, you can paste this binary value for the y-position to make the area appear near the top of the map: 0100000
You'll see the white square at the new coordinate. You can edit the area freely. If you want to hide the area once again, press B and set the y position back to 0000000