Well if you want to go with the JW fantasy of Paradise, then who really cares about our current understanding of genetics and the benefits of having a more diverse gene pool. "The Big J" would make everyone's alleles perfect so the Heinz 57 argument shouldn't factor into making the population more robust.
There'd be more homogeneity for the bulk of the world population but you'll always have clusters of individuals with less common phenotypes. So variety will always be there, its just that you won't have such large numbers of people propogating a handful of specific phenotypes (caucasian, asian, etc.).
Since this is fantasy, I hope that all women are going to resemble the best mix of Latinas, south-east asians, and Indians. Something along the lines of Salma Hayek mixed in with a bit of Tia Carrera and Aishwarya Rai. (swoon).
Back to reality. The free flow of new alleles into all the smaller gene pools is crucial to the long term health of our species. But you'd always want some almost separate populations on the side to allow newer alleles to take root and possibly drive speciation.