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.
QF is not required to offer up space on their own services due to an OAL schedule change. In this case JL is the faulting carrier... not QF.
If it were the other way around, where QF caused a misconnect at MNL where QF20 had a schedule change, then yes, QF can offer up space on alternative...
If airline staff either don't know how to do it, or aren't willing to do it, the only other way is to book with a travel agent that knows how to do it and let them do it for you.