Let me ask you this question. If you have someone co-mingling funds through various business accounts in a manner that you cannot tell one from the other - is that really a group of entities that you want to attempt to exempt from filing??
That's a question of risk appetite rather than whether it is permissible by regulation. I'd never exempt a payroll customer either, but I technically can.
Otherwise, I am not sure of your question. FIN-2012-G001 deals with aggregating for reporting responsibility. There is no relationship to that and the ability to exempt a single entity from CTR reporting. The exemption rules indicate:
The designation must be made separately by each bank that treats the customer as an exempt person
Customer is defined as "An entity that is not a legal person".
No where is there support to aggregate multiple customers for exemption.
My point is that the support is based within the interpretation of the guidance. Sure, if you're a strict constructionist, then yes, common owned entity CTRs shouldn't be considered for exemption eligibility; however, for the sake of consistency, you should also be limiting what you consider eligible to single currency transactions greater than $10,000. Conversely, if you allow for an interpretation beyond literal, as many do, then you include CTRs triggered only due to aggregation. So why stop at common ownership?
I can understand the hesitancy to aggregate common ownership because the form doesn't allow it to be filed that way. But IMHO - "FIN-2012-G003" uses the phrase "reportable transactions" to clarify their interpretation of the 31 C.F.R. §1020.315(b)(6)(ii) requirement to be consistent with how all CTRs are aggregated.
Lastly, the spirit of guidance post-2008 GAO Report has been loosening the restrictions. Examiners I've spoken to on the topic have encouraged more exemptions with less overhead. I'm not sure they're looking to draw an arbitrary line in the sand here.
To me - either aggregate everything or aggregate nothing.