Japan has some of the best (heated seats, built-in bidet, etc), and some of the worst (squat-style, no toilet paper), so on average Japan is just so-so. Of the 40 countries I've been to, the United states has the best average toilet standard.
(They would argue that squatting allows for a healthier bowel movement, and feel that dry toilet paper can never wipe off poop as well as hand+water.)
Probably not the only reason, but it definitely contributes.
Instead, what you'll find is that it tends to depend on the age of the building. There are seem to be very few examples of low-quality restrooms built in Japan in the last 10-15 years, regardless of who paid for the building.
Anyway, I'm done discussing toilets :-)