It has to be done just before a departure out of Australia.
It's because we have outbound immigration smartgates. If you don't want the passports linked / don't want to give the foreign passport details to ABF, that's fine, you just have to exit on the Australian passport / deal with your...
This is not quite correct.
For taxes that are a % of ticket, eg. AU GST, Indian sales tax and others, those are still applicable on the second seat. The other government/airport per pax taxes are not applicable.
For the same reason BR only flies to BNE and for a while ages ago, CI only did BNE as well. BNE is home to most Taiwanese in AU. Similarly, UL initially only flew to MEL... because MEL has more Sri Lankans.
Even if this is booked as a single ticket, you cannot through check from QF to CX at CGK on this connection so you have to clear immigration and collect bags. CX seems to have some weird inhibitor on through checks at CGK.
Did you book via an agent? If yes, get them to enter the FF numbers on a per flight basis.
If you booked online you'll have to chance it with check in changing it for you, and be prepared for it to go wrong.