a country's taxation law is outside the remit of EU treaties (aside from VAT), but they have powers around state aid. in this case they have tried to draw one issue into the scope of the other. Ireland has indeed offered a neat tax avoidance facility for international companies, what should be in question is whether or not this was on a special basis for Apple alone. the commision's press release is conspicuously lacking in detail what the special deal with Apple is, it explains how the internal accounting transfers profits to the "head office" account which isnt domicled in Ireland isnt due to pay tax. it even acknowledges that if the profits had been taxed elsewhere they wouldnt be subject to this investigation, contradicting the premise of state aid. i.e. if Apple tomorrow repatriated to US all Ireland HQ profits from 2003 onwards, there would be nothing to pay to Ireland.
But surely they would then owe the IRS a shed load of money.
The whole point is that Apple, and probably other large multinationals were offered sweetners to locate there. Surely that isn't taxation policy as it seems it wasn't available to all businesses as part of taxation law.