I am unfamiliar with that res system. That sounds super annoying though. At the smaller hostel I worked at we have our KD separate from our system. We have a little box where we put envelopes in with the guests name and room number. We then put the KD in there until they check out. We would charge $20 for a key since we had actual keys and if someone took one we would have to change all the locks in the hostel to prevent burglary. It was just enough to ensure people would come back for it.
At a bigger hostel that I worked at we would charge $10 and that was incorporated in the system. So if you look at someones individual booking it would show the amount they paid for their accommodation then the $10 would be added to that. The day they were due to check out their reservation would have a balance of $10 which showed we owed to them. Does Bacpack online not let you have set charges for certain things?