Are you sure that Apple will want to exclude a region of half a billion people (that's more than the entire population of the US
No, not every company has the resources to actually take these loopholes...
Sure the appeal will take some time but Apple has little to nothing to win, and the longer it takes... the bigger the amount will be (interests and no reduction should that be possible).
The government tax rate of any EU country should comply with EU regulation. Ireland is not doing any different, but Apple took advantage of something Ireland offered and Ireland didn't do anything about it (because it was supposedly benefiting it as well...)
In general the EU legislation in fiscal and economical matters has priority over any national law of any EU member. That's what make the EU special.