The article is trying to address a legal situation but uses terms like "that doesn’t mean they’re paying anything resembling their fair share" and "everyone is correctly saying Apple did wrong".

The moral/ethical viewpoint is being addressed here, not the legal one. If the law is out of step with the moral viewpoint (as it so often is), then folks on the moral side apply pressure to change the law. The law is supreme in our part of the world, and arguments that ignore it are simply beside the point.

An appeal is exactly the right way to test the law, so we'll see at the end of this process if the EU is actually challenging Ireland's tax law and its legality in the context of the EU, or if there was, in fact, some illegal activity on the part of Apple and the Irish government (as is suggested by the extant ruling).