I don't think Cook is handling this correctly
If I was his publicist, I would tell him he should say "Apple fully complies with all tax laws in every country in which we do business. As many companies do, we try to minimize the amount of taxes we owe under the law. We do not believe the EU is correct in their assertions, but this is up to Ireland and the EU to determine. If the final determination is that Apple owes back taxes because Ireland did not follow EU rules, we will pay the taxes we owe, though the EU should strongly consider whether retroactive changes to tax rates is the proper way to achieve their goals. While Apple is in a position to pay, other companies in a similar position could feel significant financial stress"
And then refuse all further comment, referring to his previous statement that it is up to Ireland and the EU to determine.