Only way I can think to get past the auto-tile problem would take A LOT of config. You could probably create a script that changes the auto-tile bitmap while the tileset is being made, but that would require you to set up the x, y, and bitmap for every tile that you want to use it for. This would be god-awful, so not worth it, and extremely tedious to setup for a single map, let alone multiple ones.
My best suggestion would just to work with the seven. In my experience I have never needed more than seven.