Now, I'm speculating that QF used the 139(3) exemption - I can't imagine that they wouldn't. [Some may recall that, when the ANRs were in vogue, this reg was 113(3), as I recall .. same, same .. just in case the reg number call out is causing any confusion].
If that be the case, the pilot does not have access to the AFM as it lives in the ops eng tech library or some similar place. The pilot only has the information in the ops manual so the operator must, necessarily, carry the can for providing the information upon which the pilot is directed to rely.
I would speculate further that the procedure hadn't gone through Tech Services and was a Flight Ops matter ? Ignoring the absence of an NTO concurrence would have produced much navel gazing in the engineering empire.
I preferred the AN approach .. the pilot exercised considerable autonomy in such decisions on the line .. just don't embarrass the boss by doing something stupid.
Curiously, I recall the complementary problem with another operator in the past. An optional mod to the fleet was assessed by maintenance only. The decision was that it was not worth the cost.
Had it gone through operations, the Chief Pilot would, most definitely, have required its embodiment. You guessed it, some time later its absence caused damage in the lots and lots of dollars region ... Needless to say, the internal processes were changed very rapidly so that all relevant stakeholders had a say in such matters thereafter.