That's more or less what was already happening; which is why the EU told the Irish government they had to stop giving Apple a preferential tax rate unavailable to other companies. Ireland didn't want to collect this money.
The "deal" is that Ireland is holding the back taxes in escrow until the appeals are exhausted. And because it's such a large amount, Ireland had to hire managers/custodians for it. The terms are probably about what the money is going to be invested in.
This is what will happen.
Its a miscarriage of international justice.