Every human base pair mutated

A memorable comment on the effects of large numbers:

If mutations occur at random over the entire sequence of a species' genome, how can a complex organ such as an eye evolve? How can all the mutations that direct the development of that:

... At more than six billion individuals, the human species is now so large that every single base pair of the three billion in the genome is mutated several times, somewhere in the population, every generation. Some of these mutations are so harmful that they're eliminated before their carriers are even born. But the great majority of mutations are harmless (or at least tolerable), and a very few are actually helpful. These enter the population as exceedingly rare alternative versions of the genes in which they occur....

The response to the question doesn't address the hypothesis that clusters of genes may have higher mutation rates as an adaptive response to a novel ecological niche.