Bottom line is that this is a shady deal that benefits Apple and Ireland at the expense of the rest of the EU. That seems to be the core of the motivation of the EU to pursue this, and I am sure the EU is using any legal grounds it can stop this kind of thing. In any case I find it odd in the extreme that Apple's R&D is in Ireland, supposedly, but all new Apple software features are rolled out in the US first even though the EU has a larger population....
Convoluted rules regarding corporations and taxation and trade that don't appear to be fair (or even that sensible) are nothing new or unique to Apple or Ireland. It probably wouldn't be very hard to find examples of lower tax rates for companies in the EU that weren't American tech corporations with large hoards of cash to pay penalties with. And that's the primary problem: what the EU is attempting to do now is something that has no previous precedent. There are no prior successful rulings against other companies operating in the EU, and that's part of the U.S. Treasury's argument against it. Basically, the EU has just invented this retroactive power over individual countries tax rates out of thin air, and it seems to be mainly targeting specific types of companies with specific levels of ready cash.