"...they almost certainly traverse fewer fiber route-miles and physical router ports (Comcast’s two primary costs of delivery)."
That is, unless the author meant Comcast's primary costs within their network, which is not what I read it as. Without providing reference to the cost of the peering, the comparing the _geographic_ distance of traffic seemed irrelevant. Even in this case, the reason that it is more expensive for Comcast to send traffic is not that is coming from Seattle, but because they are losing money on having Level3 pay them.
Edit: I also need to read more on this as I'm curious why Level3 is paying Comcast since Comcast is (as far as I know) not acting as a transit network. But I suppose this is what happens when you violate valley-free routing.
Edit2: Also, just wanted to add, the fact that Comcast controls the peering links is why this is so sketchy. By raising the costs of peering links, they could make it way more expensive for the competitors to send their users traffic, forcing the competitors to raise their prices, allowing Comcast to be the only content provider to have reasonable prices. While the part about the bandwidth to them not counting towards your cap is sketchy, the practice of charging you less, a lower flat rate, or not at all for traffic that stays within the network is reasonable. Where it is sketchy is when that difference is leveraged to make the service cheaper. If the service is more expensive, it's the fact they are charging competitors more that is sketchy. So... in general, providing content and the network is all around sketchy.