If we insist that the little girl is a victim of APTX, then her being Sera's mother is the most plausible theory IMO. Sera herself has mentioned that her and her eldest brother resembles their mother, whereas the 2nd brother doesn't look like them. Therefore, there's no way that the child who resembles Sera is her 2nd brother. And we all know that Akai is Subaru plus his hair is black, therefore the only option left is the mother. There's the possibility that Sera and Conan simply have different perceptions of what looks similar. Such a flaw is more understandable and realistic in real life but definitely awkward and wrong in a planned, idealised situation (the manga). For example, I see more resemblance between the little girl and Haibara than Sera, but since this is manga, therefore the girl resembles whoever the author intended for her to resemble and has no connection whatsoever to Haibara.
On another note, it could be that Akai was disguised as the 2nd brother (he got his blonde hair from his mother assuming that the theory above is right, so it kinda adds up), and the 2nd brother who has been helping Sera through the phone all this while was in fact, Akai himself. Since Akai was disguised as his brother, then he also probably lied about his own age and use his brother's age instead, which is of similar age to the 2nd brother's old friends (from the villa case). Sera found him when they visited Shinichi's house and lied that she doesn't know about her 2nd brother's whereabout to keep his identity concealed, which is also the same reason that he rejected Sera's request to stay with him.
This is just a theory though since it's also very likely that Shuukichi Haneda or someone else is the 2nd brother. Shuukichi is highly possible since the name is similar to Shuuichi, but then Sera probably wouldn't adopt the habit of calling Akai Shuu-nii since she has 2 brothers with that name.
Nah I don't think it depends on our perceptions but the perceptions of the characters in the manga. Their perceptions are the real message that the author is trying to get across to the readers. Read my spoiler above.
All information I can find about the Akai family states that they're American of Japanese descent, meaning they're Japanese by ethnicity and American by nationality. No where does it suggest that one of the parents is a non-Japanese. Having non-coloured hair doesn't seem to be such a big deal in the manga despite that all Japanese hair colour are naturally black to dark brown.