Portraying him as "normal" would be if none of the Japanese characters ever mentioned or referred to him being an unusual sight in Meiji-era Japan. That's what people are complaining about.
That applies to white people, too. The entire point of Tom Cruise's arc in The Last Samurai was him going through the trouble of being accepted by the clan he was being held captive by. But even in the end, the Japanese didn't see him as "Japanese". He was still a white dude.
If you're going to make a story set in a time and place where people are highly homogeneous, and you include a character that is different (even if they're just a foreigner from a different culture that still looks the same as the general population), you should pay attention to that and think about how the locals would react to said character. A black guy in Meiji-era Japan would be seen as a curiosity. Some people wouldn't even want to touch him. He'd be called names and given (usually negative) titles. It could make for a really cool story about overcoming adversity and prejudice by proving one's worth and making allies with those who are able to look past appearances. But that kind of story is getting harder and harder to come about these days.