I reckon the letter is intended to maintain support in Ireland rather than the EU, which is a lost causes. Given the rise of EU scepticism and Brexit (remembering the UK and Ireland are extremely close) if Apple can maintain support in Ireland, Ireland will continue to push back strongly and might be somewhat successful.

Of course it could also back fire with the EU (particularly Germany) playing hard ball with both Ireland and the Brexit negotiations simultaneously and any negative effects on the UK economy scaring Ireland into compliance.