Included usage is a gift with a number on it. Overage is not a gift. Treating them as one line is how invoices become arguments.
Two codes
Give included usage a meter code. Give overage a second code. Same unit, different rate, different stub.
Example: API-INCL at $0.00 for the first 100,000 calls. API-OVG at $0.0004 after that. The statement shows both. The customer can see where the gift ended.
Why footnotes fail
A footnote that says "overage billed at list" is not an audit trail. It does not say how many units crossed, at which timestamp, against which included bucket.
If you need a portal to explain a number, the number is wrong.
Credits after the fact
If you waive overage, print a credit stub. Do not edit history. The original overage line stays. The credit has its own code. Periods remain reconstructable.