why would natural selection stop at skin level?
The division of humanity into "races" was not natural.
Yes, some (e.g. darker skin in sunnier locations) was natural,
but for the most part it was the result of human intelligence and racism.
Genetic drift caused slight differences between isolated communities, but when those communities came into contact the interbreeding that would normally occur with non-intelligent species tended not to happen.
People tend to favour those that look more like them and to fear those that look different, so it's natural to choose familiar looking mates.
Beautiful people had more children than did ugly people.
Over time, each group began to look more and more like its own ideal version.
This deliberate, artificial, selection was based strictly on external features, so it was those features that eventually defined the races.
There was no such process affecting internal features, so the "evolution" you are asking about simply didn't happen.
I hadn't realized that this process wasn't already well known.
The idea certainly wasn't original to me. (I remember seeing, just within the last year, a quotation from a scientist (ethnologist?) at the beginning of a TV program that expressed the same idea, but of course I don't remember what it was.)
I've searched for references for this process and can't find anything at the moment (I'll keep looking), other than something I wrote myself a few years ago:
Us versus Them
There is something in human nature that makes us want to identify with and to belong to groups of other human beings. We can see this grouping into "us" and "them" everywhere.
Children separate themselves into girls and boys; high-school students separate into cliques of jocks, nerds, and preppies; adults separate into Masons, or Rotarians, or Kiwanis; sports lovers separate into Mets fans or Yankees fans; and so on.
Two individuals can have extremely different backgrounds and interests, but if they meet as strangers and each is wearing a Yankees cap, they experience something that links them. There is no objective reason for this; unless they have bet money on the outcome of a game it really makes no difference to those individuals, much less the rest of the world, whether their team wins. But to them it is important; if the team wins they somehow feel that they personally have won, that they are personally better than they would have been had the team lost.
This phenomenon happens at all levels. Many people are proud of their city, their state, or their country for no reason other than that they are part of those groups. If you think about it, it really doesn't make sense, but it is a fundamental part of what most humans are. (If Texas really were objectively better than Oklahoma, everyone would abandon the one state and move to the other. Texans might say that the reason this doesn't happen is because all Oklahomans are too stupid to see the truth, thereby further illustrating the "us" versus "them" phenomenon.)
From a survival perspective, this attitude has had great benefits throughout history. If someone identifies more with you than with the person beside you, they are going to kill that person before they kill you. If you are in trouble, someone that identifies with you is much more likely to help you, even if only because they might hope the same of you someday. Having other people view the world in terms of "us" and "them" increases your chance of survival.
The earliest, most basic grouping was by family. We tend to look very much like our parents, our siblings, and our children, and we feel safest in their company. If we identify ourselves by that criterion, we will also have a slight tendency to identify with other people that look like us. We will naturally be more likely to work with, to be friends with, and to marry people that look like our family.
Isolated groups will develop an ideal image of what they look like, and over time members of that group will come to look more and more like that ideal. Children whose appearance is outside the norm will be picked on, and as adults they will be outcasts. These funny-looking or ugly people will be far less likely to survive or to find mates, and over generations the genes that make them look different will be eliminated from the community.
In a world of geographically isolated settlements, after dozens of generations, the inbreeding will greatly reduce each group's genetic variability. Each group will of course have its own unique selection of genes, different from that of all other groups. Where there is contact between groups, the "us" versus "them" nature will exaggerate those differences even more. It will be easy to see which members of the "us" community have "them" characteristics, and any such children will become outcasts.
Over the centuries, this "us" versus "them" inspired inbreeding is what has created what we now call race. Racism isn't the natural consequence of the existence of race. The causal relationship is actually the exact opposite. Race is the inevitable outcome of human nature's "us" versus "them" mentality.