Just fyi, if you only include Tokyo, price nearly doubles. It doesn't make the best comparison because Tokyo + 3 prefecture = 38 million people with over 5000 square miles.
However, that chart alone is very compelling because it shows something that you don't see anywhere else; declining housing price.
Is centralized and lax housing regulations the main reason for this? I don't think the author makes a strong argument, but it's certainly a contributing reason.