If you look at how Toyota's dealership network operates in Japan (Toyopet, Netz, etc.), you'll see that Toyota is capable of vertically integrating the entire distribution chain very well. My own experience of buying (in my case a Suzuki kei model) a domestic car in Japan was quite eye-opening: my dealer came to my house and had tea with us, found us the best, least-expensive configuration of the car, dropped it off at the house some weeks later, and then stayed in touch like a member of our extended family, checking in every few months to let us know he was available. When I accidentally left the dome light on overnight night, he drove an hour each way to deliver and install a new battery, at 10PM, in the rain. And we had to beg him to invoice us. Sure enough, when I sold the car about a year later, I offered it to him first. He took the Shinkansen from Nagoya to Kyoto to pick it up, had tea with us, handed us an envelope with about 70% of the original purchase price in cash, and drove it home without even so much as an inspection. (By the way, the purchase price was $13K for a 2017 model that got around 80mpg.)
The inefficient dealership network is not something that emanates from Japan, but is Japan Auto adapting to local customs, legal requirements, and standards.