You can't take the Japanese criminal justice system out of Japan. It's part of a larger whole.
The Western mentality, especially in the USA, focuses on independent will. The government is not supposed to stop people from making choices that are bad for society or bad for themselves. In Japan, the mentality is that every person has an obligation to work with society and to fit in at all costs. The Japanese criminal justice system exemplifies that spirit, but it touches all areas, such as employment, personal relationships, behavior in public, talking to strangers, etc.
In short, if you want to have the advantages of Japan, you need to take it with the disadvantages as well.
Could you tell me how actual torture helps that system, and why exactly you can't take it away without disrupting the harmony?
It is definitely possible to hold people in detention without torturing them while also getting acceptable results.