Additional fees - HyperDia

Hi

I have found the fare quotes on Hyperdia to be a little hard to follow and wanted to make sure I understood exactly how they and the JR Pass work.

As far as I can find out JR regular tickets have a fare structure of 1) basic fare based on distance (Joshaken) and 2) Shinkansen, Express or Limited Express fees that are added on journeys on those train types (based on distance traveled and train type - Tokkyuken & Kyukoken). For long journeys on shinkansen services this is a significant portion of the total fare.

Hyperdia (I think) bundles any of the distance-based charges together with any optional charges like green car upgrades under seat fees. So, e.g., a Kyoto to Kansai Airport trip on October 31 catching the Shinkansen to Shin-Osaka and a limited express to the airport has a basic fare of Y1,880 and "seat reservation fees" of between Y1,340 for unreserved seats and Y2,990 for reserved seats giving a ticket price of between Y3,220 and Y4,870.

Can I assume 1) that the JR pass covers the full regular ticket cost (i.e. including the hefty Tokkyuken) as well as any seat reservation fees if applicable (and that seem minor in any case) and 2) the only additional fees would apply if catching a JR service that was using a private rail line?

Or have I misunderstood it all?!

Thanks