The common ownership designation was established by my predecessor at the recommendation of our external auditors,
Bad decision based on really bad advice.
The guidance rlcarey linked explains the rule; i.e. you do not aggregate based on common ownership alone. That guidance references earlier guidance that sets out the exception to the rule; i.e. if the entities are not being operated as separate entities their cash should be aggregated for CTR purposes.
Your facts do not suggest that the entities are not being operated separately. The fact that their transactions are being conducted by the same person is the only reason their transactions would be aggregated for CTR purposes.
There is absolutely nothing that says the activities of multiple entities can be aggregated for exemption purposes. You evaluate whether the entities meet the definition of an exempt person one at a time.