An alternate interpretation might be that the laws are so strict and arcane than even Apple, who seems to be trying to do everything right, is fined.
It seems like Apple clearly violated the policy it rightly should establish for any software on iOS. They deserve the penalty.
They chose to use tracking tokens in the first place. By default a computer does nothing, someone was tasked to write this. Apparently they did something wrong, maybe it was an honest mistake, but I find it a stretch to just assume or expect they are necessarily choosing what's best for users (and leaving money on the table) without more info than is public.
And this "arcane rule" is pretty much 50% of everything you read about GDPR (heard of cookie dialogs? they are not just banners anymore due to GDPR). Hardly arcane to me.