Unfortunately Japan is not very progressive when it comes to matters of race. Foreigners get treated differently and there is a good deal of bigotry against them in general. I don't know for certain but I know that white people get treated that way so I can only imagine that a brown person would get it much worse.
Japan never got over its imperial ambitions and it has a very strict immigration policy because, essentially, it doesn't like the idea of diluting its culture and national identity with migrants. Chinese people and Korean people are held in particular disdain in mainstream Japanese culture.
If you were thinking of moving to Japan, I'd investigate other people's experiences of bigotry and racism especially if they are brown-skinned before I'd make up my mind about it.
Yeah, it's pretty hardcore :/
I'm glad you did your research though!