Using NEX as connecting train at Shinagawa

We will be using a green car JR pass and will be staying in the Shinjuku area. We plan to go to Kyoto on a number of days. The Hyperdion site says we could take NEX to Shinagawa and connect with A Hikari there to Kyoto as long as we make a reservation for the NEX from Shinjuku to Shinagawa. It would be better than taking the CHOU rapid to Tokyo station but is there some rule about using NEX when one is actually not going to Narita? thanks