PC games don't need keybinders. If you release a version where the controller recognition is disabled, the game won't interfere with JoyToKey, and that will make the game work smoothly with every controller that Windows itself can understand.
I'll take a look into it, but I think the way Clickteam Fusion handles controllers is they're either on or off, and by that I mean I include the controller support or I don't. I don't think the controller extensions for Clickteam allow me to turn off detection. Obviously keybinds are an option, so that would be fine for the future, but outside of that, I think if I disable controller detection, I disable controllers in general unless outside programs were used to enable them again in a roundabout way, unless I'm misunderstanding what you're saying.