Steam support recommended some updates to controller support, which have been made:
1) You can alternate between using the controller and keyboard without selecting "enable/disable controller" in options
2) if using keyboard/mouse, the controller related graphics automatically disappear, and appear if using controller
3) if your controller is unplugged during game-play, the game will automatically pause
Other fixes:
1) removed unnoticed glitch in tutorial level
2) removed ability to kill one of the bosses by turning them into a chicken.
Known errors that have not yet been addressed:
1) if two controllers are plugged in, the game will not automatically pause until both are disconnected
2) plugging/unplugging two controllers rapidly during game-play might cause the game to stop recognizing the controllers, restart the game to fix.
Next Update:
1) Final boss will be made harder