Paypal take their fee based on the entire payment because they are processing the entire payment so of course that is the amount they base their charge on.

Ebay have now started to charge the fee on the entire payment because they can and because they want to. One reason id to stop sellers listing things at a low price with inflated postage, another is to bring the Aus site into line with the UK and US sites where the fees have been charged on postage for years now and the third and probably main reason is because they can make more money which is, after all, the reason for their existence.