It's science fiction/fantasy. If they want to change the what a genetically engineered superman looks like I think there's enough leeway there.
So if you take an Indian embryo and genetically engineer it to be superhuman, it turns into a white European dude? Yeah, I think there are some issues with that concept.
Besides, Abrams has a professional relationship with a very fine Indian actor who's popular with American audiences and would make a great genetic superman.