Actually there is no cost for FAA paperwork to do the actual jumps. The procedure for a specific jump approval is just tedious and time consuming but, other than the time invested, there is no cost. There was a large, one-time, cost for the approval for flight with door removed, flight testing, and the interior configuration.
The term for the airspace involved is actually RVSM, which is Reduced Vertical Separation Minimums, which requires very special digital altimeters, special auto-pilot, and other equipment for flights above 28,000'.
As the aircraft is used for nothing but these jumps, and would not be practical for normal jump operations, the cost of operation must be absorbed by a limited number of customers who can afford such jumps.
There are many things that are not available to the average person, or skydiver, due to cost and that is why everyone does not own a Ferrari, go to the ISS, and live in mansions. But, there are some that can and do. A private citizen went to the ISS, cost him 28.5 million. An 18 year old went up in Bezos rocket for the 15 minute flight, cost 2.8 million. Virgin Galactic ride to the edge of space sold out 800 slots for $250,000 each, now the ride costs $450,000. Very special things take very special money.
Michael Mullins