"It is, however, proper application of Bayesian evidence."

Nonsense.

If the only relevant pieces of information you had were the race of each man, and the average intelligence of each race, then of course it would be rational to estimate that the man from the 'smarter' race were the smarter of the two. But this is very far from the truth. In the Obama-Bush example, there is more than enough evidence on the public record to swamp any racially determined prior.

I think the principle of 'treating people as individuals' exists to combat a couple of things. One is the tendency to form stereotypes on flimsy or non-existent evidence, to over-estimate the generality and force of those stereotypes that are factually based, and to treat prejudice (i.e. group membership-based priors) as a substitute for even very easily-gathered and reliable evidence about the individual. The other is the direct emotional harm done to people by treating them as members of a group first, and individuals second (if at all). It is possible for this harm to outweigh the benefits of otherwise-rational discrimination.