That is actually incorrect. JL has been charging fuel fines on AU-JP flights since last year. It used to be 42 AUD per AU-JP flight, and is now 83 AUD.
Since JL bookings weren't possible online previously, unless you had access to the PNR or the ticketing data, you wouldn't have realised that JL were indeed charging such a fuel fine.
See JL fare rules:
Code:
ORIGINATING AUSTRALIA -
IF THE FARE COMPONENT INCLUDES TRAVEL BETWEEN AUSTRALIA
AND JAPAN ON
ONE OR MORE OF THE FOLLOWING
ANY JL FLIGHT
FOR TICKETING ON/BEFORE 31JAN 18
A FUEL SURCHARGE OF AUD 42.00 PER DIRECTION WILL BE
ADDED TO THE APPLICABLE FARE.
AND - FOR TICKETING ON/AFTER 01FEB 18
A FUEL SURCHARGE OF AUD 83.00 PER DIRECTION WILL BE
ADDED TO THE APPLICABLE FARE.
The above rules apply to all JL commercial fares in all classes. QF is simply passing the charge on from JL.