The flight could have been legally operated with two crew if they had made a “tech stop” somewhere along the way; for example in Darwin. Not very efficient, but legal! This has been used in the past when operating two man crew back from the Middle East i.e. Bahrain to Hong Kong, with a “tech stop” in Dubai to cover the AFTLs.
A pure guess, but perhaps the company offered this option OR, ... “if you like we have a dispensation for you to go direct? What would you like to do?”
Either way, good to see the AOA challenging this!