Actually, that's a good example of the problem here. For the longest time, in the US, benefits weren't considered income. So you could get health care coverage, use of a company car, and none of those things ever got mentioned on a 1040. Then the law changed (and I'll admit I'm not sure if it was an IRS ruling or legislation that went through Congress) and suddenly workers did have to declare them - but only some. And they DIDN'T go back and say "everyone owes taxes on that stuff before the rule was changed. Meanwhile, free coffee, free water, on-site cafeteria aren't taxed.
I'm not an EU law expert. If the EU law is "no tax incentives allowed", then yeah, the case is cut and dried, Apple and Ireland are in the wrong and back payment may be reasonable. If it's a lot fuzzier, "can't be too good", so there's a judgement call whether it's a "subsidy" - the EU has the authority to make the judgement call that this condition is "too good" and stop it going forward. But unless there are specific guidelines that were clearly broken, trying to enforce that judgement retroactively and require back payment is unreasonable.