A question for @bjorn: Does the automapping feature replace every tile in the map with a single parallel pass? Or does it do tile by tile in a sequential manner, and for example, when the second tile is processed it already takes the changes made to the first tile into account? That makes quite a difference for how to define the automapping rules.
Also vermadead have you found any solution to this? I would like to use automapping for border generation as well, because our tilesets don't have transitions between every possible floor type and whatever tile type requires borders (to define those seems very wasteful when we dont need them really).