Ye gods this whole thing is silly.
In America, dark skin is associated with slavery, racism, and discrimination. Blackface and whitewashing are pretty big deals here.
In Japan, dark skin is associated with gyarus and the Japanese equivalent of rednecks. Farmers get dark skin from working in the sun. Same with manual laborers. Okinawans, who live close to the tropics and get a lot more sun, also often have dark skin and are considered country bumpkins for some reason. Dark skin isn't associated with race.*
IIRC, 97% of people in Japan are Japanese and a significant portion of the population has never met a foreigner. That's the actual reason they import teacher's assistants from English speaking countries - it's not so much to teach English as to expose the kids to someone that's not Japanese. The Japanese population as a whole doesn't understand or care about the whole European vs. African thing or the whole history of African slavery and discrimination.
This manga was created by a Japanese artist for a Japanese audience. Stop trying to shoehorn your own cultural baggage into it.
* OK, native Okinawans are technically a different race, but Japanese people tend to think of Okinawans the way Americans think of West Virgianians for some reason.