The emphasis on fresh high-quality food made me wonder if that sort of food is more satisfying (and filling) than what the author sees in American food. Does eating poor quality food leave you hungry? (Also, consider people living in “grocery deserts” who subsist on large amounts of fast food. Their obesity rates are very high.)
From what I remember when I lived in Japan vegetables weren’t a problem as much as fruit was. They were either seasonal, expensive, or both. Also the fattier, red meats could be difficult to find (things like pure ground beef was uncommon and was commonly found as a beef/pork hybrid).
And yes, I would imagine public transportation (or just having to walk/ride a bike) is a huge boon to overall health levels.