Were you able to choose your own input layout, or does the engine require this particular one?
You can define the layout however you like. It works by assigning actions to keys and buttons. Within the game there's currently no way to determine if, say, "up" was pressed via the arrow keys or a controller d-pad. I suppose you could define a distinct set of actions for controllers only but I'm not sure why you would.
If you were to release a version of the game where the controller recognition is disabled, that would be enough to open up enormous controller flexibility, as long as that doesn't disable the keyboard functionality too. For example, in the RPG Maker XP engine, there's a screen where you can disable every item in the Gamepad category, but that won't affect the Keyboard one (I provided an image).
