Of course it does. Now why EU should finance foreign company trying to circumvent local taxes like some chinese sweatshops vs local massive company that gives work to hundreds of thousands local people?
US does exactly the same, also in car manufacturing. This is normal market behavior, countries protect their companies. Apple has nothing substantial in EU, completely foreign force milking the market and paying nothing in taxes. Now if they opened big factories and research centers, they would be treated very differently but they prefer Foxconn or other chinese companies.
Ireland having tax sovereignty was doing what it felt was best for itself, the low tax ecosystem it has fostered is in its benefit. Much like car and farming tax incentives favour Germany and France respectively.
Now perhaps the EU as a entity is moving towards collective taxation policies, but it's not there yet and there's still an aspect of getting away with certain fiscal policies depending on any member nations "clout". Perhaps Ireland is mostly guilty of not having said clout.
