That's what I thought you meant. So use of the bounce protection feature would indeed create an overdraft of the employee's account.
Your question about whether or not these overdrafts should "count" against the employee in light of your policy is a good one. My suggestion is that the policy (which probably existed before bounce protection) needs to be updated to account for the existence of bounce protection.
Here's the approach we take. It may or may not work in your environment:
If the employee is eligible for bounce protection and has opted in to the servce, the employee is free to use it within the same parameters as any other customer. The same limits apply, and the same expectation that the account will be returned to a positive balance apply.
If the employee uses the overdraft service excessively (as defined by the FDIC guidance) and requires counseling (again- following the FDIC guidance)- the counseling is handled by Security, and HR is notified. Any account-affecting actions (such as removing bounce protection) are completed using the same parameters we apply to our other customers.
If an employee overdraws their accoutn in excess of their bounce protection limit, or if the overdrawing employee is not eligible for bounce protection, HR is notified of the overdraft, and disciplinary action in accordance with our policies would apply.
So in summary- in our policy, we do differentiate between bounce protection use and other overdrafts.