I might be reading more into the original post than is there, but, I think that there will still be static as the OP follows the guidance in the Q&A.
Yes, they can file DEP on the agency, and that means the undercover officer's information won't go on the CTR.
No, the undercover officer isn't completely off the hook, since the last part of guidance suggests that the bank record enough identifying information about the officer to ensure that they're actual LEOs. The undercover agent is still likely to become cranky that the bank is collecting identifying info...
Just my US$.02 (which is worth less and less against leading currencies all the time....)