Yeah, the concept of having earnest money for higher priced auctions is a good idea to add to ebay, but it might discourage some people from bidding because then you have ebay sitting on your money in some sort of escrow until you need it for an auction.
While fast, a ACH transfer still takes a couple of days to settle, so if you needed the earnest money up front and there are only a couple hours left in an auction you might be in trouble. Or maybe you'd need to use a CC or something to have the cash available right away in your 'earnest' account, do it as a hold instead of a full settled transaction.