Please follow this link for my tileset.
It took me a while, but I have figured out the 3x3 bitmask and how I can use it in my game. For those wanting to use 3x3, here is how you set it up.
Assuming a 64px by 64px tile tilemap, create a new image with a size of 1536px x 704px.
To get consistence with your individual tiles, stamp the tile from my image (see link) which is 100% filled (row 2, cell 1) and flood-fill it to your entire image. Then, select all of the transparent pixels from my image, copy, and paste onto your spritesheet. This will create your new tileset.
Now, resize your spritesheet by 200%. This will create a tileset of 128px x 128px tiles.
Add the spritesheet to your Godot Tileset. Set the Autotile Bitmask Mode to 3x3. Set the Snap Options Step to 64x64. Then, go through the image and set the bitmask for each sub-tile.
Save. You now have a properly designed 3x3 tileset.
