The Global Hotkey (first image) is for turning listening on and off. In your case, since, 'toggle' is selected, if you press ALT+F2 listening would first be turned off and on again with each subsequent, 'hotkey' press.
A command shortcut, or, 'When I press keys...' executes the command that it is associated with. In this case, it always turns ON listening. Since there is no check to see if there are conflicts (design choice), the global hotkey is executing first and then the command... which always turns listening on.
The solution would be (as you've already pointed out) is to remove the, 'start listening' command.
Hope that helps some