Anime and manga that focus on competition often have a far-away goal for their protagonists, and in many cases that final obstacle is something or someone foreign to Japan. In American football, it’s African-Americans. In Go it’s Koreans. And in multiple instances of boxing, it’s guys from Latin American countries.
Takamura in Ippo and Yamato Takeru in Eyeshield 21 are both said to be unusually large for Japanese men, as if to use the exception to make the rule. According to Hikaru no Go, Go is treated much more seriously in Korea than Japan. Like in the case of Starcraft, Korea apparently has a more robust infrastructure which allows it to create superior players. While not always strictly a matter of genetics, these masters are often portrayed as having some sort of amazing inherent advantage over their Japanese counterparts. The Japanese characters often have to either realize their disadvantage or use something inherently “Japanese” in them to try and make up for the skill gap, though keep in mind again that Japanese-ness is usually not genetic but rather a learned trait from growing up in Japanese society. At times the Japanese X-Factor will be family, friends, perseverence, hard work, all things that probably anyone Japanese or otherwise can relate to, though they seem to have a strong place in Asian cultures in general.
Rooting for the underdog is something that’s been spoken about by countless people since long before any of us were born, and I think that certainly plays a factor, but I get the feeling that this specific method of portrayal of an underdog while not strictly Japanese is also something that is not surprisingly a product of Japanese entertainment, especially Japanese entertainment geared towards boys. While I do not think Japan as a society enjoys being the victim, would it be a stretch to say that Japan has wanted these stories since Commodore Perry arrived and perhaps even before?