This seems simple enough. If you are doing updates (OTA or not) to software that is part of the car certification then each update needs to be certified as well

This seems simple enough. If you are doing updates (OTA or not) to software that is part of the car certification then each update needs to be certified as well and regulators need to be on the lookout for cars running uncertified updates. I'd be surprised if this wasn't the case already. OTA introduces nothing new to the problem. Car dealers do software updates during service regularly already.