Zerodha does not collect penalties on a client-by-client basis but rather as a collective sum for all clients. Therefore, Zerodha cannot provide a specific acknowledgement from the exchange for the penalty you paid. Zerodha acts as an intermediary, collecting margin penalties from clients and passing them to the exchange.
The brokerage industry is heavily regulated, and exchanges and SEBI conduct multiple audits on brokers. These audits include reviews to ensure that brokers are not misusing client funds, such as charging penalties and failing to transfer them to the exchange.