(Note: Having finished writing this, I remembered that Matt Thorn wrote an essay on this issue, and googled it, and, uh. It looks like a lot of what I’ve said is just regurgitating stuff he said. Sorry, Mr. Thorn! Here, go read that.)
Most manga set up one or more “default ethnicities” within which the mangaka feels free to give the characters a pretty large range of physical variance - as in, members of the “normal” group can have whatever hair and eye colors the mangaka feels like (as long as they’re black and white, I mean), various facial shapes, and slightly dark skin (if the mangaka’s not allergic to that). CLAMP, for example, generally gives the full range to Japanese, Chinese, European, and mix-thereof characters. In this way, the Japanese and Chinese and English characters can’t be physically distinguished.
Then there might also be one or more “non-default/exoticized ethnicities.” An exoticized ethnicity isn’t allowed the full range of variance - some attribute (90% of the time hair color) gets coded as a racial marker, and can’t vary within the ethnicity. Example: The volume of CLAMP’s Tsubasa where they go to a Korean world, and everybody has black hair.
(Actually, I think that Kurogane’s feudal-Japan world is also limited to black hair, which raises questions about the human tendency to exoticize/racialize our own histories/ancestors…)
The more typical example, found in 90% of manga set in in modern-day Japan: Bisco Hatori in Ouran High School Host Club gives the full range of hair-color variance to Japan, but limits European or European-Japanese-mixed characters to blond hair. Hence the weird dissonance between the art and the writing, where people say that the mixed-race Tamaki and Nekozawa “stand out” and have a “foreign flair” because of their pale hair - while plenty of pure-blooded Japanese characters like Honey, the twins, and Haruhi’s dad also have light-colored hair.