Maybe it's just me, (cuz it IS late) but I don't really get what you're asking??
Ebay is the selling venue...Auctiva is just the listing service (at least for right now). Of course you are always going to have to pay Ebay/Paypal fees no matter what, listing is not free.
You can have ebay without Auctiva, but you can't have Auctiva without ebay. Make sense?
As for your last paragraph, I don't have an ebay store so no opinion