(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.
The defaults vary within a mangaka’s work depending on setting and what the mangaka is trying to achieve. Osamu Tezuka drew Chinese characters as squint-eyed Western-style caricatures in Ask Adolf, set mostly in WWII-era Germany and Japan, but in Tezuka Default Style in Boku no Son Goku, set in folklore-ancient-China. Yuu Watase’s manga are mostly set in Japan and involve no non-Japanese characters or discussion of race, “allowing” her to give her characters a wide range of hair colors. Her Sakura Gari, however, limits its Japanese characters to black hair, presumably because one of the two protagonists is mixed-race, and a good deal of the plot revolves around this. (Sakura Gari is also set in the Taishou era, while most of her other works are set in the present day. See: exoticization of history again?)
(Incidentally: Ask Adolf’s default ethnicities are German, German-Jewish, and Japanese, so those groups are drawn in Tezuka Default and are not readily distinguishable. The Nazis can’t tell from looking at him that the half-Japanese guy is half-Japanese, allowing him to join the Gestapo and so go crazy with guilt and identity issues and so forth. I don’t recall whether people within the story can tell the full Japanese characters from the full German ones, or whether the half-Japanese guy gets taken for white or Japanese in Japan.)
A lot of Western readers get confused as to whether that slight-tan thing that some manga characters have is supposed to indicate race, and why even manga like Petshop of Horrors, ostensibly set in a large US city, don’t tend to have any characters recognizable as black/Hispanic/Indian/etc.
The reason for the latter is that - to put things very crudely - Japan is racist to the point that most mangaka cannot draw these groups. The mangaka I’ve used as examples above all use basically the same techniques for racial identification of Asian and white characters. These techniques are part of manga’s basic visual vocabulary, in the same way black panel borders mean flashbacks and light reflecting from a character’s eyes means danger.
Western readers, when we first get into manga, tend to get excited about the depth and flexibility of this vocabulary - but the fact is that this vast, extremely codified vocabulary, which a mangaka must know and be able to use in order to get published, doesn’t have the words for non-Asian-non-white characters. They don’t get drawn enough for those words to be necessary.*
For the former, my experience is that the tans are just tans, and more what a Western** reader would call a class marker than a racial one. Generally, the tan is shorthand for “working-class/uncultured/trashy.” I would imagine there’s some association with the ganguro subculture (which manga tends to associate with working- and lower-middle-class girls - not sure if that’s the reality), but given that it’s also used on male characters, and there’s a fair amount of social taboo against dark tans in Japan, I think it’s probably more complicated than that. (People with tans = people who have to go out and work in the sun = lower-class? People with dark skin = tanners = burakumin? Dunno.)
Because the tan is already coded as a class indicator, it can’t be used as a racial one without carrying that baggage along with it - Fullmetal Alchemist is the only example I can think of that actually does use it to indicate race. Revolutionary Girl Utena makes use of the type for Hey Let’s Subvert Some Even More Stuff purposes - it is Not Done to make the dark-skinned characters rich, polite, cultured kids of impeccable lineage, and certainly not [spoiler spoiler]. (Also, one of them’s named Ohtori, which surname in Japan apparently gives off vibes like, I don’t know, “Muffy Vanderbilt III.”)
* To stall off anyone considering writing a sorrowful comment about this is in my comments - no, the West isn’t much better off in this regard. Most Western artists cannot draw an attractive dark-skinned person, because the techniques they’ve learned and their ideas of beauty are all intended for the depiction of white people.
Because I’ve been brooding about this issue’s applicability to Second Life skins all week, I offer you up this example (slightly NSFW, scroll down to the bottom for the “black” one). This designer is extremely popular and well-reviewed, but all her dark skins have this unattractive ashy coloration - she seems to just do some sort of color-replace operation on her pale ones, not realizing that darker skin doesn’t reflect light the same way pale skin does. (I won’t go into the facial contours of her model, as there are some sensible reasons for a designer to display all her skins/clothing on the same shape.)
** I specify “Western reader” because, basically, the way race is constructed in Japan is complicated, and I don’t feel competent to try and come up with better vocabulary for this phenomenon.