I don't have access to the AFRs analysis or to the records Apple provided ATO.
It is certainly undeniable that Apple has been create in its tax accounting. It uses the "double-Irish-Dutch" scheme and some have said that it invented it. That, however, is beside the point.
A crucial point - almost always overlooked in sensational media releases such as these, is that thirty years ago Apple took a bold step in its development strategy. One that has paid off in this instance. That step was to allocate expenses for development of its intellectual property (the most valuable asset) between the U.S. [maybe North America] and the rest of the world. Each division was charged a portion of the cost in proportion to the share of sales. This started in about 1980 or 1981 - I'm not sure of the exact year but it certainly was before the introduction of Macintosh which was 1984. So "Apple US" paid its share for devices sold in the US [or North America] and "Apple Ireland" paid its share for devices sold in the rest of the world.
So the point is that we don't know - and AFR is probably not interested in finding out - whether or not this profit is just a reasonable return - to Apple Ireland - on the years of development expenditure it has incurred.
I acknowledge the point that Apple has been creative in structuring its corporate organization to minimize its taxes. There's no fault in that. If the Government wants to change it then let it change. Until then it is what it is.
If AFR wants to assert that Apple has acted illegally with use of "transfer pricing" etc. then it should make that claim and let it play out in court. I'll wager that it [AFR] will never do so because it would expose its somewhat shoddy investigative and reporting practices.
Game on, AFR !