You know how you can turn an estimate into an invoice. Maybe you can make a module for Receipts, which converts an invoice into a Receipt.

In the Recurring Invoices you can set it up so it will Create, Charge and Send Invoice, when in fact it should Create, Charge and Send Receipt. The definition on Receipt is: An acknowledgment (usually tangible) that payment has been made. So maybe you have the following modules / pages in the left menu: Estimates, Invoices, Receipts and so on.

The difference between a Receipt and a Payments Received is that the Payments Received module doesn't show each item that the customer purchased.

A receipt will basically be an invoice, with the word Receipt where invoice was and a clear indication that the invoice has been paid.