Seat Fares?

The seat fare is included. (see: http://www.jrpass.com/forum/topics/general-japan-travel/posts/what-is-the-seat-fee)

I have a related question and do not want to create another topic. Is the seat fare still included when booking via jr-east (https://www.eki-net.com/)? Because my reserved seats display a "Seat Charge" but state "Pass Type: JAPAN RAIL PASS" as well. Why would the site tell me about a charge which I don't have to pay?