Why Apple doesn't really care that much
Let's illustrate the point with some made up numbers. Let's say Apple does business in three countries, the US, Ireland and country X. They make $3000 in the US, $2000 in (or funneled through) Ireland and $1000 in country X. They pay 40% in the US, 1% in Ireland and 20% in country X.
Their tax bill for last year would then be $3000 * 40% + $2000 * 1% + $1000 * 20% = $1420. They'd carry a future tax liability of $2000 * (40% - 1%) + $1000 * (40% - 20%) = $980 on their books for when they bring that income from Ireland and country X back into the US.
If the EU made Apple pay 10% instead of 1% to Ireland, they would pay an extra $180, for a total of $1600. However, their future tax liability would DROP by that exact same $180! In the long run their tax liability would be the same.
There's one catch - they could be collecting interest on that $180 while it sits overseas. In fact they do, they invest those huge overseas cash holdings. They're in super conservative investments though, and Apple earns an average of about 1% on that cash. Which in this example would be $1.80/yr.
Of course, the EU isn't trying to make Apple pay an extra $180, but an extra $13 billion, upon which they currently earn around $130 million a year. Most of us would go to court to hold onto $130 million per year in income, even Bill Gates. If they lose, they're only out the cost of their lawyers, and they probably have most of those guys sitting around or on retainer anyway. Wouldn't you rather have them fighting the EU than sue Samsung again? Especially if you voted for Brexit, and hate the EU anyway :)