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"If I am booking on Qantas, it seems like I get much more bang for my buck by booking with a Qantas FF number than a BA FF number. Is that correct intuition?"
The answer to that question depends on two factors:
1) How many miles (or Avios) would you earn in each program, taking into account the booking class of your QF flights?
2) How many miles (or Avios) would the respective programs require for the type of award redemptions you are contemplating?