That total is pretty close when you add the times for Shinosaka-Shinagawa via Hikari + connection time + Shinagawa-NRT on the N'Ex. I just figured that you had already paid for the rail travel with the JR Rail Pass and the flight option is an extra expense. The other factor, which may not apply in your case, is that I refuse to fly in the cramped space that is Japanese domestic economy class. I would rather spend some extra time enjoying an eki-ben and watching the scenery go by. Again, YMMV.

Don't change plans on my suggestion. Just offering options.