These rules and laws esp. with regards to visas and immigration are not about the rules themselves. They're a proxy for government to be able to control the types of people they think benefit their society (and whether or not to let them in the country). If you fit within those concepts of what is deemed acceptable, no one will bother you.
Are you a rich, white professional class person with a first-world passport? You have signalled that no one needs to bother with you. Things like visa regulations will be applied less strictly.
If you are from the wrong country or you are the wrong skin tone, your chances of having a bad time are much higher.
This applies not only to Japan, or countries like Thailand or Mexico, but also to the USA and Europe equally.