FYI, I'm using the 3x3 minimal settings on https://github.com/godotengine/godot-docs/issues/3316#issuecomment-614923124
It seems to be auto tiling cell 10,0, maybe it should be using 9,3? But that doesn't solve the vertical walls.
For example - in your screenshots, the walls perfectly line up with the "grid".
But in the tilesheet, the vertical walls go down the middle of the tile?