Rip Off??
Yes and No
The Sudanese Nav fees are correct, they are a fixed fee for all flights up to a certain weight. It is dangerous not to pay, you could be banned from overflying
The Handling fees in Zanzibar are standard rip off for using use a "Supervisory" agent.
In Africa (except in a few places) why use a handler? Somebody always comes out to give a hand for a few $. If you really feel uncomfortable about that pick up your
AC-U-KWIK and book your own handler and save a $1,000.
The rest of the fees are normal for obtaining overflight clearances. Again you can always do them yourself if you want to save the money,