From Paypal's perspective, they are charging a fee for moving a certain amount of money from one accoun to another. They don't, and rightly so, care what the purpose of the money was. On Ebay's side (the auction side), they do now charge fees on the total transaction. They excluded shipping cost for a really long time, and probably would have stuck with it, if it weren't for shady users actively reducing their own fees by inflating shipping charges to the winning bidder.
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