Hyperdia showed the route from Shinjuku to Kameari as:
(1) Shinjuku station to Nishi-Nippori station via JR Yamanote Line
(2) Nishi-Nippori station to Ayase station via Tokyo Metro Chiyoda Line
(3) Ayase station to Kameari station via JR Joban Line.
The last "transfer" at Ayase station where the Metro Chiyoda line changes to JR Joban line is a not actually an actual physical transfer but where the same train from one line continues to another line, so there's no need to get down.
If I have the JR pass, I don't have to pay for the first leg of travel because it's the JR Yamanote Line. However, getting on the Chiyoda line at Nishi-Nippori will require me to pay when passing through the transfer gate but notice how it changes to JR Joban line after Ayase station? That would mean I got on a Non-JR train at Nishi-Nippori and "transferred" (without needing to physically tap my Suica at a transfer gate) to a JR train for the 3rd leg of travel.
My question is: When I come out of Kameari Station, how much would they charge me? Since I have the JR pass, the part from Ayase station to Kameari station via the JR Joban line should not be charged. But if you are using the Suica to transfer at Nishi-Nippori and then tap out at Ayase, would you have to pay the last leg of the journey which you shouldn't have to?
