Shinkansen price on navitime

I’m trying to understand how Navitime app comes up with their pricing. I’m checking Shin Osaka to Nagoya. It’s showing :
Nozomi
JPY 3410
JPY 2530 - non reserved seat
Below that there is a button for buying shinkansen & express train tickets, showing JPY 5940

However, when I clicked that button the price on the website showing JPY 8670 for unreserved seat.

What caused the price difference?

JPY 3410 = base fare
JPY 2530 = shinkansen supplement for a non reserved seat
JPY 5940 = total fare if you buy the ticket through JR

JPY 8670 = total cost if you buy the ticket through Navitime.

In other words: Navitime seems to be trying to charge you a 46% service fee!!!!! Stay away from them by all means!

Wow, thanks Uji

The JPY 8670 price is what you pay if you buy from a third party with a huge mark-up rather than from JR. There is no need to pay such big premiums, but there are some companies that charge like this.
As a footnote, before you could book/buy online for these services I did ticket buying for a few clients and certainly charged a lot less for the service as those premiums are just huge.

I understand you can get discounted tickets if not travelling in busy Japanese holiday period on the day of travel. My question is do you ask the JR ticket counter for discounted seats on certain trains that day or do you buy from another seller?

Non-busy period discount is fixed in the fare and might be 200 yen on a 14,000 yen ticket (Tokyo<->Kyoto)