As I say in the piece, both Apple’s lawyers and accountants and the Irish government’s people agreed that this was all legitimate and above board at the time. That’s the most you can ask of Apple — that it did all it could to ensure it was in conformity with applicable laws at the time in the country in which it was doing business and liable to pay taxes. The EU actually has no direct say over this as it happens – only the investigatory and review power after the fact. That’s why this action now — especially reaching so far back into the past — is so egregious. There was no way for Apple to know that the EU would respond this way many years later.
If Apple’s actions with regard to repatriating income were really analogous to individual tax dodging, as you suggest, the IRS would long since have intervened (as anyone who has ever paid their annual tax late can attest). But the IRS hasn’t. It’s entirely legal for companies to keep their money offshore if they choose to do so, and Apple is making tax accruals in the meantime based on reasonable assumptions. You call it blackmail, but you might call it leverage — Apple isn’t the only company in this situation, but it’s using its clout to push for changes here. Again, nothing wrong with that.