I had this issue booking a J award through to Halifax(YYZ) via JFK. Even though it was the same points to either JFK or YYZ; I would still be charged the 2500 if I booked to YYZ as that had to be done by phone.
After 2 calls and a supervisor I had it waived. The supervisor did agree it wasn't entirely fair.
Not sure that going through this every time you need to book an award tic, where destination hasn't been loaded to online bookings is good PR. Would it really be an issue to upload all OW destinations onto the system??
If any QF bods who are part of this forum could respond would be great or perhaps take it up internally.