Probably, Akutagawa didn't want to project that image on to a Japanese person. It may not have been as popular if he made his main character, a prostitute and strongly religious Christian, Japanese. Also, it might have been harder for the readers to picture themselves in that situation.The antagonist had to be foreign and not speak Chinese, and probably to be unable to place what nationality he was, making him half was the easiest way to go. As for American-Japanese, there were probably a lot of American/Japanese people at the time, and the image of Americans probably weren't that good either.The reason for choosing Christian over Buddhism was probably again for the reason of ambiguity. It probably wasn't a well understood concept, and Akutagawa could play with it all he wanted as a writer.
Also, my favorite character was the Japanese guy that appeared twice in the story. He was the most sane and down-to-earth person in the story which is also something I believe that Akutagawa wanted to portray. It's kind of the like feeling that he wanted to say: "Of course the character that makes the most sense is Japanese." I think.
@コートさんthe Japanese guy ・・・その人は芥川龍之介じゃない？
Good point! I never thought about that, but that makes even more sense of why that character seems more realistic and why he would like his readers to relate to him.