I've lived here 13 years & am raising 2 girls who both have been able to live in the manner described in the article.
1) The number one reason why we feel comfortable is the number of "safe" people constantly around. In Japan, every apartment building of size has maintenance people who stay several years and know all the children in the neighborhood, and recognize strangers. Every supermarket has parking attendants. Every construction site has "guards" to make sure people cross the area safely. Every train station has staff around. Many grade schools have patrols of parents who literally "sweep" the neighborhood right before school lets out, just checking that no "out of place" people are hanging around in the parks and neighborhoods.
What this REALLY adds up to is like the article said - there are always people out there keeping an eye on things.
2) "Japan is safe" - yes, but assaults on children/young people are a problem, and parents worry. My first point prolly rules, but we are still selective in when & where they can do that. We make sure someone is meeting them on the other end. It IS safe, but not all "roses".
Just my thoughts