Like I said the "innocent" and "fair" Apple.
And the outcome is against Apple because Apple
challenged the Commission.
Taking in consideration so many Europeans work at Apple I would say its impossible they wouldn't have known that their deal with Ireland, the preferential treatment, tax cuts are not legal and accepted in the EU, but their American bosses most likely didn't care. And FYI companies in the EU can get state aid in very specific cases but it has to be approved by the Commission. For example, I know a company that just built a factory that is the first in the world of it's kind with zero CO2 emission. State aid was approved by the Commission because of this.
And what Ireland thinks is irrelevant, they can't go against the rules of the EU.