I have spent some time on this subject and it is often we visit onsen albeit the same routes given the timeframe. However, there is a website named YADO, a group of so-called owners of Authentic Japanese-style inns, those who preserve, foster and promote the heritage of Japanese inns around the world.
In Japanese, the word ‘yado’ refers to a traditional inn: https://yado-resort.com/#
Also I snipped apart and photographed a recent version of Crea March 2018, and all is documented below by photographs from the magazine. If you wish to check a location enter the phone number into your search engine and it will likely show up the webpage although many are in Japanese.
Otozure Ryokan /far from Tokyo/ Haneda airport to Yamaguchi Ube airport is 90 minutes/and then from the Airport to Otozure destination is 70 minutes by Taxi (12,500 yen).
T. +81 0837-25-3377