Yes, state aid laws are old. But they were put in place and are intended for situations where governments are subsidising weak local companies or industries that wouldn't survive if exposed to (intra-EU) competition unsubsidised. That's why they call it "aid".
But nobody is arguing that Apple is weak and needs to be protected from foreign competition in this case. Apple is the foreign competition. And Ireland isn't paying them money to keep them afloat. So this is a very different sort of situation to what state aid rules were designed for, and that's why the EU is using such a tortured definition of "aid". The Commission has wanted to control and harmonise member state tax policies for a long time but know governments would never let them when asked directly. So they are finding ways to bend old powers to their latest needs.