That's plausible. Indeed it would be pretty hard to break even without an alternative business model: books usually have a MRSP printed on the jacket and charging more than the MRSP is unusual; plus the rent in Ginza is over 400usd per sq m.
I used to work at an independent bookstore that had a niche for local and regional(WV/Appalachia) authors and stories. This worked great as we were in a tourist area, so the influx of new customers was readily available.
For local customers we offered custom orders, to address issues with limited supply. Though it would be cheaper to go to Amazon, a large portion of the community are artists and craftsmen so they liked to encourage the local economy.