Hmm... I never thought about this. Is there a reason built-in controller recognition is a problem? I never considered it being an issue.
Built-in controller support is a nice thing, if you're using official Xbox (or, less commonly) PlayStation controllers. People like to give those controllers plug-and-play value. However, for controllers that are more generic than that, I don't like seeing an Xbox layout imposed on them, because I don't have the ability to create my own layout, no matter how generic the controller is. Some games include a keybinder, but they don't absolutely need that. Running a game alongside JoyToKey will work too.
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.