Actually, you don’t need to give up your JR pass when you make reservation by phone. I bought only limited express ticket (特急券) and sleeper ticket (寝台券) by phone reservation. I can take Twilight using JR pass with the tickets bought in advance.
If you go to Midori no Madoguchi and ask for Twilight using JR pass, they will charge for express and sleeper surchages (特急券 and 寝台券). So, this works perfectly when you make reservation
using this service.
When you use this service, please don’t forget you can pick up only from JR West station