There's not much uncertainty for business really. If you're pulling the moves that Apple and other companies pull to "optimize tax", then you are with 100% certainty trying to game the system and violating the spirit of the law.
They just found that Ireland's tax rules from 1991 and 2007 are illegal tax benefits according to the preexisting rule.
Just because they took so long apply existing law doesn't make it retroactive.
This is a retroactive ruling. This is playing favorites, the opposite game.
Same with the data contracts with the US, Safe Harbor, Privacy Shield etc. All approved, all later on found a violation of EU law.
That's not retroactive just slow.
The central difference of opinion is of course whether outright gaming the system is acceptable regardless of the written rules being followed to the letter.