It is a bit odd
Back in the dim and distant past, when software came on media as well as online, Adobe used to fulfil the media orders from Scotland and the electronic ones from Ireland.
IT was often a few pounds cheaper to buy the media plus shipping than the download just because of the VAT levied. The UK was cheaper than Eire.
Oh, the wonders of the Tax System. Ask 10 accountants how it works and you will get 20 different answers.
As the VAT returns have to be done quarterly and vert little remains with the people you are buying from then I'd be incluned to give apple the benefit of the doubt here. Whatever is the case the VAT paid to the Dublin Government by Apple, Adobe, Microsoft, Google etc etc etc must be considerable.
As for Luxemburg, then I go ask a certain J. C. Junker about it all after all he set it up before becoming WU President. I guess it is safe to say that his home country won't be investigated in the same detail as Eire.