What you say is true. But there is some good news. If you go to a 3rd party cart (some are free) then you can calculate that value and put it several places, the best of which is the "handling" variable which overrides any PayPal calculated handling charges for an item.
The other advantage of a 3rd party cart is that when it sends items up to PayPal the user cannot change quantities - the cart is frozen at checkout time.
Here is a client-side example so you can see how it works (this one sticks the charges into a dummy item entry)...
http://members.aol.com/paypalcart/
Ron.