Apple isn't headquartered in Ireland, Apple Sales International and Apple Operations Europe are. The EU says these subsidiaries have been making untaxed profits, but it's not obvious that they've made any profits, ever (that's the whole point of the tax scheme in the first place.)
The grey area seems to be that there has been a cash hoard in Ireland which legally is on the Apple Inc. balance sheet, but hasn't been taxed. Again, however, Apple Inc. is not domiciled in Ireland so it's not the Irish governments job to collect that tax.
What am I missing?
Are they completely legal or is this just a case of they are legal, until a court finds that they actually aren't legal.
Even if they are legal, I would argue that convoluted schemes to avoid paying taxes is unethical in the same way that moving manufacturing to a place with lax environmental or labor laws in unethical. Apple might be able to make phones with what is effectively slave labor legally, but they shouldn't.
To the extent that things are generally legal until they aren't.
The complaints from the US treasury are that the decision goes against pre-existing case law, and so shouldn't be applied retroactively. [1]
A 'power grab' is an adequate description of what's going on; the EU commission is basically forcing member states to redefine their own arm's length principle and their application of it. They would call it 'tax harmonization.'
1] https://www.treasury.gov/resource-center/tax-policy/treaties...
It's not about lower taxes in general, it is about lower taxes for a single specific company. And that constitutes state aid which is (mostly) forbidden under EU rules, as it is massively uncompetetive.