Ok here's the break down with the reserved seat charge, its a combo effect.

The base fare between Tokyo and Kyoto by any shinkansen train is 7980yen, then you have a limited express fee tacked on depending on distanced traveled, then you have a seat reservation fee which is typically 500yen (around 5us dollars). The Limited express fee is often bundled as a "RESERVED SEAT CHARGE" on timetables, so that probably explains why it shows as 50plus USD dollars, which is the approximate limited express fee to kyoto from Tokyo.

If you have the JR railpass you pay ZERO. But only for Hikari and Kodoma Shinkansen.

I don't like world eki much, since if you miss the train they still charge you, even with the railpass, also pick up locations are only for JR EAST stations. No luck if you want to pick up tickets at Kyoto or Osaka stations which are runned by JR Central and JR West respectivly.

"Which one is the donald duck nose"
Thats the Series 700 trains.