The rule is if the companies are different legal entities, their currency transactions are not subject to aggregation simply because they have common ownership. There isn't anything that suggests that a known pattern of structuring changes your CTR filing requirements.
Yet, here is a FinCEN
ruling from a few years ago where the owner was basically ignoring the entities' existence, transfering and moving funds around like a shell game. In this specific instance, FinCEN said the cash was subject to aggregation because the entities were being treated as a single enterprise. Your example does not sound so extreme as this one, I would continue to treat them as separate entities for CTR filing.
Your consideration of a SAR and a potential account closure seems to be on the money. These folks are consuming enormous amounts of your employees' time in order to play this little game.