Unfortunately that's a limitation of the way Godot handles inputs by default as far as I know (when inputs are bound to the same "action", holding down one of the inputs bound to it will mean that pressing a different bound input won't activate the is_action_just_pressed() function, which is used for hitting notes). There might be a way to fix it by making a custom input handler, but that's quite a bit more work. I'd like to do it at some point though