I don’t understand this question since in fact if you have two terrain types, all possible transition variations account for 16 tiles (given there are 4 corners that may each be either terrain). Where does the 9 plus inside corners come from?
Not at the moment. You pick your tile size for the map and that’s what Tiled will work with. If you want to treat the tile size differently in the game logic, that’s up to you.
The RPG Maker VX map editor basically uses the tiles as 32x32, but it has special logic for the terrains. With the terrains it is making combinations that are in Tiled only possible when using the tiles as 16x16.