Nit: I’m not sure this argument is completely sound. You’re saying that the genes that account for visible differences make a small percentage of total genes, therefore bigotry based on these genes is very unlikely to be justified since it would only be justified if these genes themselves were extremely important.
Another possibility is that the genes that account for directly observable differences, while themselves insignificant, are highly statistically correlated with more “important” genes. If this were the case then it might be a lot more likely for one’s bigotry to be “justified” than the raw percentages would suggest.