Jed, might be worth a try but as the Act specifically applies to ships not aircraft the ATO would, I think, be reluctant to part with our cash.
In regard to the employer/ employee issue, my understanding is that this referes to the employer withholding tax to pass to the ATO. I believe this is how the process used by employers in Australia is described and how your tax usually gets paid. Ideally a foreign employer would withhold the correct Australian tax if if you are an Australian taxpayer. Of course in practice this usually does not happen and you get hit up for the difference later.
The incentive for the employer is that they can genuinely advertise for Australians, pay them the same pay as a local employee, and know that the take home amount is competitive. How many people looked at Jetstar Asia and then immediately discounted that as an option because the numbers didn't work paying Australian tax rates.