There is no legal requirement that a bank must have a system for aggregating cash transactions. There never has been. However, it would be nigh on to impossible to audit BSA compliance in the absence of such a system, so they are a regulatory expectation at least.
Regardless, no bank has a "perfect" system that aggregates cash "by or on behalf of the same person" at every possible portal. As no system is required, there are no "exemptions" for the portals that are missed in one system compared to another.
What might be helpful to you is to hear from other bankers whose ATMs cannot recognize the composition of a deposit as to whether their reviewers thought that was a significant shortcoming. To sit through such a criticism, I would have to hear someone pointing out instances where the amount of currency we missed was significant.
In this world you must be oh so smart or oh so pleasant. Well, for years I was smart. I recommend pleasant.