I think this is BS. They get to charge you for a VIP you don't need. Ask them to explain the physics of it.
Actually, that fits into the theme of this thread:
About 2 years ago, the shop was very reluctant to fill my buddy's dive-tank that was low, around 200psi. We were able to "convince" them after a little arguing, but it did leave a bad taste in my mouth.
More recently I got my VIP certification. Just to be on good terms with the shop, I explained I had just received my VIP cert, just VIPed the tank, and that's why the tank was empty. The owner was okay with that (as he should be) but then said "you know why we won't fill empty tanks, they should have covered that in your class.." I didn't want to argue and figured, maybe I had missed something, so I didn't really say anything.
I asked my instructor, and he quickly responded that no such requirement exists.
The best I can think of, is that an empty tank may suggest a diver screwing around with their own equipment, and you might want to double-check that the valve is secure or that no debris is in the tank before filling for safety reasons. However, that wasn't anything my instructor mentioned.
Personally, I have a couple more reasons to be annoyed at this dive-shop, but unfortunately I don't really have other practical options for fills at the moment. And I get the vibe that if I did try to argue with him, he might refuse my VIP stickers, and there are probably better hills to die on.