Once you're off in jumpspace, the Captain will raise the issue. The crew can either agree to the deduction or not (and do without). IUAEGMP (Interstellar Union of Astrogators, Engineers, Gunners, Mechanics and Pilots - pronounced ew - a - gump - but everybody needs to have their letter in the name so we are stuck with it) rejects this practice.
Yes, there are a lot of ways the trade system could be complexified, which might be more interesting sometimes, but on other occasions would only get in the way when you're try to get the players to focus on other stuff. For my money, it is better if the Referee just decides the exceptions. Realistically, market forces and other factors should be pushing freight rates up and down anyways so the fact they are fixed is unrealistic.
