The former is not that surprising considering how safe Japan is. The latter however is a known social issue. Oyabanare (leaving the parents) is the term for independence, and many have a hard time.
Physical independence is a step every toddler takes when they learn to cope with not having their parents around during day care and such, and in Japan it simply extends to the commute. Traditionally, the Japanese would not even lock their doors. The entire community is an extension of their living space, with lines drawn with respect, not fences or locked doors. So just as you wouldn't call a child independent for being able to go to the bedroom and back, going to school and back is the same but farther, with the community acting as a safety net to ensure these children commute safely. Kobans also help (community police manning one man police stations that patrol on bicycles).
Psychological independence unfortunately does not extend naturally from the above. With many young adults being too dependent on their parents and on instruction, they suffer from the inability to think or act or speak for themselves. They can commute fine alone. They can be hikikomori fine alone. They are fine alone. They just are not independent in the western sense. They are afraid to act on behalf of themselves or enact their identity. So they also resort to 2chan and anonymous free speech which does not help them gain a voice.
Westerners are almost too comfortable acting on behalf of themselves. It is almost a given. And that is also why parents are less inclined to "let them loose" because "loose" is what they are. They are free thinking and free acting, hence a long solitary commute only sounds dangerous. But it is this perception that instills that very quality in their children. The perception of being on an infinite leash yields physical freedom and distance, but to confuse this with psychological independence is an egregious mistake.