Another thing they value is to not make change until one is certain it is actually an improvement, and they assume existing rules were made with the same care. The above can be very frustrating because there's some changes that are obviously for the better and some rules not made with the best intent or carefulest consideration.
But the idea that Japanese are all cowards dismisses that the demure personality comes from a collective cultural agreement that requested change must be thoroughly considered, and that it is in some way implying the previous makers of a rule were unwise or lacked consideration. So to propose a change without being what they'd consider a brute or idiot would take maybe more energy than that person is willing to give for the issue.
Who accused Japanese of being cowards? People here are raised to avoid conflict and let things go. It's not cowardly, it's a useful way of keeping a community together. Unfortunately, it also a tool for めんどくさい人 to get their own way.
I don't think so. I'd say 90% of the time they don't know who set the rules or why they are that way. They just follow them to avoid attracting the attention of the local busybody, there's always one. That extends to many situations in Japanese society too, it's why you rarely see people confronting, eg troublemakers and bullies in public, or until somewhat recently, at work. They'd rather ignore them and get on with their day than become a target.