This is where we really start to get into the weeds of Japanese law and so on. What you are quoting is a "tsuuchi", or notification. It does not supplant the original law, but is only a suggestion. It is not enforceable. Further, local hotels and agencies often go too far and also ask for copies of ID from residents of Japan (like me), which is absolutely forbidden.

Even worse are outside agencies asking for such information. Scans are easily copies and stolen. ID theft is a huge problem, I would never scan any important information and send it to a business.