As a French guy who lived in Japan for some time, I've got a very simple explanation for why Japan has more Michelin stars than France.
If you go to a normal average restaurant in France, the food will usually not be very good, they will serve dishes prepared with pre-made sauces from Metro, they won't serve anything amazing. There's a very big discrepancy in France between normal restaurants priced less than 20 euros per person for lunch without wine and the gourmet more expensive restaurants.
People also go out to restaurants a lot less than in Japan so there are less restaurants in France. In Japan, Osaka has 16,000 restaurants. Tokyo has 55,000 restaurants. Paris only has 14,000.
Even restaurants that are not very expensive (1000 yens lunches) in Japan tend to only use homemade ingredients. They don't use pre-made sauces. The average quality of normal restaurants is much higher and a lot of the Chefs at those restaurants are actually passionate about the food and try hard to improve their skills.
So, it's simple, Japan is a country with at least twice the number of restaurants per population as France and with a much higher percentage of passionate chefs that want to improve their skills and are there for the love of food rather than for earning money. It's actually surprising that Japan still has so little Michelin stars.
As for michelin stars, I actually trust the Gault et Millau guide a lot more in France, they don't care as much about the atmosphere and the service, they care about the food and ultimately that's the only that matters for me.