Yes, ED gives a bit of the profit to Link, but on the other hand, Link does repairs for his customers so ED doesn't have to do those, so that probably more or less compensates. I don't think eBay will be prepared to provide free RMA services for the PandoraED makes less on the 1 Ghz Pandoras to resellers like Link than he would by selling on ebay - was one of the points.
eBay is nice if you don't have an online shop yourself, so you have a trusted 3rd party that handles the payment and selling (and bidding process if you want that) for you. I don't see the point of using it if you already have an online shop - why add middle men if they cannot give you anything that you don't already have yourself?