I'm not surprised by this. The European Commission's original decision was based on a technicality related to the fact that Apple did not use the "classic" double-Irish arrangement when setting up their companies in Ireland, but instead used two branches of the same company. If Apple had set up the double-Irish with two separate companies (like most other multinationals), there would have been no question that what they were doing was perfectly allowed under Irish and EU law.
I was always skeptical that this decision would stand up under appeal, since the argument that they received a special benefit from these tax rulings (relative to other multinationals) never made much sense. They were actually worse off under this arrangement than they would have been if they had just done the proper double-Irish in the first place, like Google and Microsoft and everyone else.