I ordered some from them this past weekend. I don't know how they're doing it, but I was charged a flat rate of (I think) $8.95 for 5 or 6 comics that I ordered from them and the method was something like FedEx ground. Like you, I noticed that they say they have the book owner ship to them and then they ship to the customer. Considering all those books need to be shipped to them and then from there back out to us, well, that's a lot of shipping charges that are obviously built into the book cost. The folks selling these are obviously the ones taking the biggest hit which goes a ways towards explaining why a book with Overstreet value of, say, $25 has an asking price of a few dollars more than that. By the time you make a counter offer you get worked back down to the guide price and the seller is in the end making a little less than book price.
I also find it interesting that a lot of the same comics on ComicConnect as also listed on Metropolis. The EXACT same books.