A better analogy would be finding that someone deliberately and knowingly claim mileage expenses at an absurdly high cost per mile in lieu of a larger annual bonus after discussing tax efficient solutions with HR. Would they face a revised tax bill for past years and be expected to stop overclaiming for future years if an authority with more standing than their employer got involved? Of course. Does Apple's team of tax law specialists have more understanding of the potential for such a scheme to be ruled illegal than the average employee? Of course.
they are being forced to buy the car that they won't keep as well.
Following your borrowed car analogy, Apple finds a gas card in the glove box on the first day and uses the car every day for 4 years and uses the gas card. When it's discovered that the borrowed car is stolen and the gas card wasn't Ireland's, who has to pay the gas card off?
Losing the benefit, sure. Paying back taxes that don't exist nor asked for? There's a problem in there somewhere.