Well as far as default layers are concerned, I took into consideration that in programming, a lot of variables in my experience have been zero-based. I got used to the idea of starting everything with zero because when it came to layers in zelda, 0 meant "zero height". All my maps use layers -2 through 2, -2 being used for parallax background tile patterns (such as horizons and summit tiles), whereas layer 2 was for overlays (such as the forest canopy and fog).
You are right about the door cache patterns, almost all of them were set to layer 2 by default. I intended for them to be layer 1 by default but forgot to double check. The door tops are on layer 1 by default, but can be adjusted to layer 0 depending on whether or not you need one for the lower layer. I have updated the data files for the tileset package.
I have included a preview image of a cave room created with the tilesets. The borders' palettes have been changed to resemble the other borders, with the exception of the brown and ice cave tileset palette, as they had colors for which their default palette was designed. If these look how you like, I'll repackage them with the Absolute Dungeon Tileset package, but I want to make certain they do so no one has to download constant updates to the tileset if they are in the process of making maps from them
As always thank you for proofing my work. it helps to have someone with better eyesight than my own to find and point out any errors there may be