It's straight forward.
- To disincentivize MH over QF on the kangaroo route (which is MH a key money-spinner, too)
- So QF premium fares retain... a premium frequent flyer earn
The difference in fares on MH/QF can be 1000's on a biz/first class Europe trip. As a consumer, you need to weigh up the overall product experience, frequent flyer benefits and determine which best suit your lifestyle.
However it's also important to note that as a QFF# member flying Malaysia - QFF will still earn the same revenue from MH (marked airline pays FF airline on each ticket), so even though you're earning at Y levels, QF will still receive the full J revenue from MH but chooses to award you less.
So either way, Qantas doesn't mind who you fly so long as you use QFF#.