Yes, Europe breached a sovereign country's ability to tax when they hit Apple with a $14.6 billion dollar tax bill. If they were going to tax Apple like this, they would have been taxing them a certain amount way before now. They wouldn't hit them with the tax amount all at once.
The European Commission’s attempt to bring Apple to heel is on the surface about tax, but in the end about the power of the multinational and the power of the state. There is more to come; Margarethe Vestager, the Danish commissioner who is leading the charge against Apple, is warming up to take on Google.
Europe versus the giants of corporate America will be a battle royale and one that will run and run.
Companies who move operations in order to avoid US taxes shouldn't be given a free ride because they move to another country. Other country's are not interfering in sovereignty if they have a legitimate case to make that they are due money based on a company using their resources. Individual companies can follow suit.
If Apple chooses to do business in Europe, they must pay Europe's taxes. It would give foreign companies an unfair advantage if European companies doing business in Europe had to pay taxes, but foreign companies, such as Apple, could come in and sell products for lower prices because they don't have to pay taxes.