My uneducated guess would be that rent and labor are much cheaper (in relative terms) in Japan than in the US, perhaps so extremely that it dominates compared to the marginal cost of producing food.

I think rent and zoning make a huge fucking difference here. You cannot really have a tiny noodle shop under a home in the US where that's incredibly common in Japan due in large part to national permissive zoning. You've got to maintain a separate home and business property and have the means to acquire or rent both. That necessarily drives up cost of small retail business and tilts the economics far more in favor of very large companies like Walmart or chains like Panda Express.