If you went and bought a new car for $50,000 and then needed to return it and get a refund you wouldn't be very happy if the dealer gave you $45,000 back and said "Sorry, the salesperson gets to keep their commission. They earned that money." The dealer wouldn't be very happy if the salesperson said "No, I'm keeping my $5,000. I did my part and I earned that money." If there's a refund then everyone gives their part of the money back.

Apple were part of the transaction, so if there's a refund they should return the money they earned. They can't just ignore the customer's wishes to get the money back, and they can't just pass the loss on to the developer. Neither would be fair.