Hollywood has unfortunately exported American-style black animus to the world, so I wouldn't be at all surprised if Japanese are more racist toward blacks than whites, especially American blacks. Also, the whole light-skin, dark-skin thing was never unique to Europeans. But relative to their general prejudice against foreigners any heightened prejudice might not be very discernible.

Dunno about more or less but when I was in Japan I saw Japanese people get up and move, not just to a different seat, but to a whole different part of the train carriage, when a couple of white Westerners sat next to them.

Also I'm guessing you're missing a 'not' in the last line there?