It's not quite the same. The tax isn't owed to the EU, it is owed to Ireland. As far as I'm aware this sort of deal is not only legal, but common in the U.S. The rules broken here are the ones against excessive "state aid". These are defined as selective advantages given to companies. The treaties forbid these as anti-competitive. This mainly applies to subsidies to individual companies, but also covers sweetheart tax deals like these that aren't open to all companies. They're welcome to set low corporate tax rates, but not to approve convoluted structures like these. Stuff like Tesla's deal with Nevada would be illegal in the EU.

More like the federal government telling you ten years later that you and Texas shouldn't have made that concession to you and asking you to retroactively pay back taxes for the last ten years.

That is exactly what the IRS does. Do you think businesses want to keep 7 years of transactions? No, they do not. And if they fail an audit it increases to 10 years.