When you refund correctly, you refund the amount you received, ebay refunds the fee making up the full amount.
It is best if buyer opens a not as described case, then you just click to refund, if youwant damaged item back before refunding then you have to supply a reply paid label, if no return required, then you just refund.
Even a partial refund now gets a partial refund if selling fee.
No fees are refunded in the event of the reason being out of stock.