eBay would say - correctly - that whether a buyer bids on a listing or makes an offer, the price they pay includes eBay's buyer protection fee. 

The confusion arises because when you sell through a listing, the buyer pays eBay's buyer protection fee in addition to the sale price. But when you accept an offer, the price offered is inclusive of  the buyer protection fee. So when eBay has taken this fee the seller receives less than the full amount offered.

From the number of questions and complaints we receive it's clear that many users dont understand this, and sellers in particular often feel cheated. So far, eBay has shown little inclination to change it, or to explain it more clearly.