There's a fairly recent article in Yahoo News about train companies stepping up enforcement of backtracking restrictions. It mentions that the penalty for fare evasion is capped by law at 2x the fare that should have been paid (plus the fare itself, for a total of 3x) -- which, I must admit, seems miniscule compared to the penalties that exist in other countries.
https://news.yahoo.co.jp/articles/ea...343aa84?page=1

They are focusing on certain stations where the practice is especially common, but it's a general prohibition under the contracts of carriage. JR says that within major metropolitan areas, you can take any route you want "as long as it doesn't overlap itself," and you will be charged the lowest point-to-point fare.
https://www.jreast.co.jp/kippu/1103.html

There are some limited cases where JR allows backtracking, but only when the passenger is on a train that passes through their destination station without stopping, and even then it's only allowed for certain stations (e.g. you can backtrack from Shinjuku to Yoyogi, but not from Shinjuku to Shin-Okubo).
https://www.jreast.co.jp/kippu/1105.html

I have breached this provision of the contract many times, e.g. riding from Ebisu to Shibuya to catch the NEX...