That is actually a good question brlmnd.
First, thanks for the absolute dungeon tileset update! I answered on gitter but I copy my answer here:
There is only one thing to improve to make autotiles work really out of the box. They already work (I use them), and by the way I can provide you the updated .dat that defines them
but the thing you should do to improve it is:

Filling the transparent part of these concave corners. Because the auto-tiles algorithm cannot guess that 8 pixels of them should overlap with edges.
However, important thing, can you still keep the current ones (with transparents parts) in the tileset as well? They are still useful in some cases (there was a good reason to make them like this in the first time).
I can provide more details if you want, but basically, for the interior tileset we now want both versions of concave corners.