The revered Manual inserted the word "denomination." The regulation does not. Your bank needs to comply with the regulation, not "the Manual;" a currency exchange is simply a reportable transaction.
Put a live CTR on the screen. Post the entries. (The report will not ask for the denominations.) If the report includes them in the math (it will) I'm not certain how the doofus who is disagreeing with you can say they are not reportable.
_________________________
In this world you must be oh so smart or oh so pleasant. Well, for years I was smart. I recommend pleasant.