I obviously don’t know how every airline works, but surely all aircrew are in receipt of allowances that are “folded into” salaries as described by the ATO as a taxable part of your income?
No they are not folded into anything they are separate. In the 'good old days' they were paid in cash by the hotel. Each airline has a different way of paying them these days but the principle is the same.
They are not considered income by anyone except for maybe a few cool aid drinking management types and a few angels who have no idea how aviation works it would appear.