Too many people are unaware of the constant mobility of populations and people across the world. Historically, trading routes such as the Silk Road have brought people of all colours and complections into all sorts of places. It is by no means impossible or unlikely to find a Black person in Japan. Nor is it impossible that such a person be made a Samurai by a daimyo of sufficient rank.
Most of this seems to be outrage for the sake of outrage. Probably doe by people who are not themselves gamers. By 'gamers' I mean people who put the quality of the game before such minor issues as the race or gender of the protagonist.