Yes. The actual gameplay is subjected to a kind of "Xbox plug-and-play" input model, whereas the menus use a generic model.
Generic models make it impossible to cleanly pair a game with a profiler (like JoyToKey) unless you include a way to disable the generic model. In this case, there's no need to include a disabling option, because the gameplay already takes an excellent approach, because it does a perfect job of reconciling Xbox plug-and-play, with generic controller friendliness.