It's a new feature so thanks for the feedback! I'm working on adding out automatic loading/unloading via circuits, so the inventory item status was meant to be part of that so the train could detect when the vehicle had finished loading or unloading. Sorry it had unintended side effects!
I'm curious about your setup--do you have vehicle wagons attached to all your trains that run normal routes? If the empty wagon had no slots, and the full wagon still had a slot with the vehicle in it, would that be better for you? It would still defeat the "Cargo empty" condition. Do your applications allow the use of item-specific conditions or do you need the generalized cargo full/empty conditions?