The set stairs isn't any different than the operate jetways option. All it does is set the stairs into position. GSX has no way of knowing if you plan on boarding or not at that point. As for the baggage train, it's empty when you first start GSX because it's assumed the first thing you're going to do is de-board the plane. It has no way of knowing that you plan to start from boarding, so the empty baggage train has to leave first before the new one arrives. So those aren't bugs, those are as designed.