The other day, I took a train trip from a station just outside the Kyoto city boundaries to Yokohama using the Nozomi Shinkansen for the Kyoto–(Shin-)Yokohama portion. I noticed on my outbound journey that if you are connecting from JR regional trains, you can directly transfer to the Shinkansen part of the staion by buying the appropriate ticket after feeding the machine your regional journey ticket (an IC card in my case).
On my return journey, I used that to my advantage, taking a JR train from Yokohama to Shin-Yokohama. I was also able to transfer through the ticket gates directly to Kyoto JR station to board my local train. However, getting off at my final station, I had to buy a fare adjustment ticket for the final local train portion at my destination station.
Question: Since I already knew at the time of purchasing the Shinkansen ticket that I would take an onwards local JR train, is there any way to purchase a ticket for the entire journey, eliminating the need for fare adjustment?
Or is fare adjustment the only and expected way to transfer from Shinkansen on to local JR trains?
Note: Please assume a non-online purchase spontaneously on the day, if it matters for the answer.