Hello!
Yeah it's a bit confusing. Let me give a working example.
If you use a tile size of 24x24, the tiles are saved in a grid of 24x24 + 3 pixels, ie 27x27 pixels. So in Godot your TileMap should use 24x24, and your TileSet should use 27x27 pixels. In reality the tiles are bigger than 24x24 pixels to allow for the dark outlines, otherwise you would have a dark outline between every tile, and that wouldn't look very pretty.
You also have to manually put in the 3x3 bitmask in Godot for Autotile, but that only takes like a minute. Here's a screenshot:
