This article is citing another article from the same source [1]
"The typical Tokyo metro area starter home would be an apartment (around 750 square feet) or detached wooden house (around 970 square feet) located in the outer suburbs. According to Zoe Ward of Japan Property Central, the average Tokyo office worker has about a one-hour commute by train each morning."
So part of the answer is that homes are tiny by American standards, and it's not actually in Tokyo proper.
A lot of the people with hour-long commutes are not going long distances by American standards. They live in "Tokyo proper" (which is really more of a prefecture than a city) or the neighboring cities.
Even square footage isn't a perfect metric for cross-national comparison. For example, furniture in Japan (at places like Nitori) is often designed for smaller spaces. When I lived there, a $300 couch fit[1] perfectly in my living room, while it would've looked hilariously undersized in any North American house. I was more comfortable in that apartment, approx 480 sqft, than I was in a 1000 sqft apartment I had in North America
"The typical Tokyo metro area starter home would be an apartment (around 750 square feet) or detached wooden house (around 970 square feet) located in the outer suburbs. According to Zoe Ward of Japan Property Central, the average Tokyo office worker has about a one-hour commute by train each morning."
So part of the answer is that homes are tiny by American standards, and it's not actually in Tokyo proper.
[1] https://www.curbed.com/2016/6/21/11946606/starter-homes-swed...