Sorry, I didn't get a chance to come back to this last night. But yes, Godot expects you to interact with a single tile at a time instead of where 4 tiles meet. And you are correct, it is an insane number of tiles if you want a full set -- 256 tiles are needed just to connect 2 terrain types and that number grows exponentially for every new terrain type. That said, most of the layouts are only about 47 tiles and that gives you more than enough control. Something like this:
But like I said before, this is a Godot issue. Definitely not a Seliel issue. You are providing a crazy amount of tile combinations. A full Wang set is already more than enough. And it's not a big deal to work inside of Tiled then bring the assets back to Godot. I just figured it was worth mentioning since other folks might also want this for Godot.