Back in 2013 I asked a question here: Returning Overpayment and have just tried the same procedure, only being able to resolve using the solution I posted.
The scenario is where a customer pays for an amount accidentally, therefore there is no invoice to allocate the refund to having tagged the inbound payment as an amount with No VAT to their account.
There is no option (showing) to just refund which would allocate to the overpayment.