ATO has been tracking aircrew allowances since Keating was the Treasurer.. Most of it is tax free. It is based on the Commonwealth public service tax free allowance system. Get paid more, the excess is taxable; get paid the same or less, it is tax free.
Difference being that there was never a way of proving what you spent your allowances on as it was given in cash. Now there is a way of tracing your spending.
The reason they are tax free is because the assumption is that they are 100% spent on work incurred expenses. If however the ATO could prove this wasn't the case....