That's generally true of all bathrooms in the USA vs Japan. I think I've seen 1 disgusting bathroom in Japan a restaurant/mall/store in the more 15+ years I've spent there where as in the USA it's like 1 of 5 that's disgusting. In other words, it's not unique to train stations.
That said, the bathrooms between JR Shinjuku and Marunouchi-line used to smell pretty rancid. I haven't used them recently though.
Oh, I agree it's not unique of train stations. The Japanese overstaff pretty much anything - it's likely part of the reason for their massive public debt, but it helps maintaining infrastructure to good standards. It's the opposite attitude we see in most of the Western world, where public resources are cut to the bone until (and often even after) things rot and fall apart.
JR East covers not only metropolitan train services in Tokyo but also a wider real estate/retail portfolio and all of eastern Honshu, with about 46k total employees.
That said, the bathrooms between JR Shinjuku and Marunouchi-line used to smell pretty rancid. I haven't used them recently though.