When using a keyboard, the act of switching between WASD and the arrow keys is not a big deal. However, being able to use only WASD throughout the whole game (for movement) is useful for keeping your control list as short as possible. The shorter the list, the less work it takes to bind a controller to the game.

Disabling the built-in controller support won't increase the number of controllers that can work with the game, per se. There are already hundreds of controllers that (technically) work. However, the way in which they work is excessively coercive, because the game imposes a generic layout. If the built-in support was disabled, I would be able to take the keyboard and mouse defaults, plug them into a profiler program (like JoyToKey) and have total liberty over the layout. It's true that some games include a built-in keybinder, which is fine, but no game actually needs it. A built-in keybinder also requires users to use a keyboard on the first launch.