The final rule makes reference to
FIN-2012-G001 which indicates that we "may" need to consider aggregating transactions for businesses that have common ownership if they are not operated independently. In FinCEN's mind, we may have greater knowledge of commonly owned businesses by inquiring about beneficial ownership at account opening and consequently, more CTRs that are filed as a result of businesses not being run independently.
Each institution must make its own determination regarding what is "independent" vs. "not independent." In your first question, the fact that Jim is a beneficial owner of each business does not automatically equal file CTRs for aggregated transactions. Look at the guidance again. Are these businesses sharing employees, have a common address, are comingling funds? If the answer is, "no" you would only aggregate transactions for these businesses if the same person made deposits to each that exceeded $10,000. I can't tell you whether a CTR is required if John makes a $6,000 deposit to business A and George makes a $5,000 deposit to business B. If they are operated independently, then we do not have transactions by or on behalf of one person exceeding $10,000. No CTR.
If, based on your due diligence, you determine that they are not operated independently, then aggregate and file.
Also in the final rule, it is noted that an owner prong person may double as the control prong. If you identify and verify both partners as beneficial owners since they own 50% of the business, then why should we be concerned about the control prong? If they are both signers on the business account, it doesn't really matter which is placed on your form for the control prong. You are not going to verify the same person twice.