Actually, the EU has truly some powers over governments, it's Apple that should have none.
The EU treaties explicitly assign to EU bodies some powers over the participating states - and by approving treaties government explicitly assigned them to the EU -, including control over competition, and ruling about state aids are within those powers.
It looks to me that even in the US most taxes are collected by IRS at the federal level, and it overpowers the single states. EU is not at that level still - but to become a true union, yes, it will have to go in that direction as well.
But Apple instead should have no power over governments, while we see large corporations (Apple, Google, MS, etc. etc.) dealing directly with state officials to write the rules (or ignore them...), and well, dear Cook, that's exactly what it is destroying democracy and equality before the law. Those "animals more equal than others" - and of course all those pigs privileges were in the pure interests of the other animals...