For auto tiles, Godot expects every tile to have a base terrain type. Tiled, however, doesn't care what terrain an individual tile is, only what terrain it is adjacent to. Because of this, you have to jump through a lot of very awkward hoops to set these sheets up to work with Godot's auto tiles and terrain system. And even when you get it working, it's a little buggy. This is a Godot issue. But most other sprite packs I've downloaded have a more Godot-friendly layout (albeit significantly less detailed than what you provide).
The difference is more obvious when you go to draw terrain. In Tiled (and maybe other editors) you're drawing terrain at the corner of 4 tiles. In Godot, you're drawing terrain on single tiles.