The EU legislation has precedence over Irish one in economical and fiscal matters. With this knowledge any other statement of you falls apart on its own. The EU is similar to the US in many things, but also different in many others.
Ireland is a country who belongs to the EU and is subject to the EU legislation. Apple can ignore the EU legislation... but that doesn't mean it is not affected by it (in fact it is actually taking advantage of it because it is avoiding being double taxed when selling in the single market...).
Apple has made a deal with Ireland that is considered, as per EU law, an illegal aid from the Irish state. The EU allows internal tax deals of its members as long as they don't go against the EU legislation, and Ireland went too much into that (and of course Apple didn't care much either since it was benefiting from it).
Now Ireland is obliged to get all the taxes Apple didn't pay when it was supposed to (a pity though that the EU can only go back a decade... but it is a good lesson for Apple and many other companies who consider doing the same in the future).
Note again, Apple was presented with a deal by the Irish government who is subject to EU law (and so is Apple, don't come here saying that Apple signed something with Ireland, if you operate in the EU soil you are subject to every single law from local one to the EU level).
Enjoy Apple, I can't laugh enough at the face of Tim Cook and many US high level people lobbying to get this not to happen. In the EU, we care about taxes, yes. That's why we have such social welfare. If a company makes money on our soil, it will pay every single penny of tax.
Oh... and you clearly didn't get anything about UK voting out (which doesn't mean it will ever happen because it was a non-binding referendum just for your information...). Moreover, those who voted out are precisely the big chunk of population who miss the old empire times and didn't care about the new generations who are actually pro-europeans (as many companies there who will move out should UK enact the corresponding article to leave).
Read a bit... before stating so many untruthful things about this matter and the EU. Clearly you don't know what the EU is.
Take it easy mate. I know very well what the EU is and live with its massive bureaucracy every day. And I know that we love taxation in Europe - Google the Danish tax system, we are some of the highest taxed people in the world. I said I wasn't in the details, so no need to go hating so much...
EU is pretty damn far from perfect and is growing bigger and more complex every day - and for a country like ours - not growing in popularity. And no, I'm 31 and it's not only the elder generations that doesn't love everything coming out of Bruxelles. I have read the voting sides from the UK but that's democracy and should be respected