I don't know what the parent comment had in mind, but here's why I think it's a dumb move: the EU just announced to the world that they can override the decisions of the member countries retroactively and at will.
If you want to invest in something in an EU country, you might calculate the taxes due on your investment before deciding if the investment is suitably profitable. With this decision, you now have an unexpected new risk factor to take into account: the EU bureaucracy may retroactively change your tax rate. That means uncertainty of payout, therefore the investment has a lower payout, therefore you are less likely to invest in an EU country.
It wasn't "just now". The rule against privileging single companies is a rule of the Treaty of Rome. Which was first signed in 1957. And by Ireland in 1973. Also the recovery of unlawful state aid is nothing new but established practice.
A better way of minimizing your risk factor would be hiring tax lawyers who know the rules of the EU Single Market. Which makes Cook's comments so baffling: Apple should have known that there is a possibility of a crackdown.
And Apple just got punished for what Ireland did, and is paying Ireland for the privilege. This makes dealing with EU countries a much more problematic venture. Countries trying to improve their economy can't introduce new legislation without it being suspect. Also, Europe was benefitting from that money. Moves like this will cause American companies to repatriate their money so the EU doesn't decide to come up with another number when they are looking to balance a budget item. How do we pay for all of these refuges? Sue American companies...
If you want to invest in something in an EU country, you might calculate the taxes due on your investment before deciding if the investment is suitably profitable. With this decision, you now have an unexpected new risk factor to take into account: the EU bureaucracy may retroactively change your tax rate. That means uncertainty of payout, therefore the investment has a lower payout, therefore you are less likely to invest in an EU country.