it seems to me that you end up getting African clusters that can be as far apart from each other as they are from Europeans. <
I doubt this would be the case as measured by fst. Note that distance on a principal components graph is not the same as fst: the components might be optimized to separate the clusters of choice (optimize the directions in gene space which show the most variance between the groups). It's possible in principle that some groups (e.g., pygmies) in Africa have been as effectively separated in gene flow from other Africans as, say, Nigerians and Europeans. More likely, the fst distance between any two groups of Africans is less than the distance from the Yoruba to Europeans or E. Asians. That is what happens when you analyze the (better studied) sub-population structure of, e.g., Europe and Asia. That is, no two groups in E. Asia are anywhere near as far apart as they are collectively from Europeans (and the same for any two European groups vs distance to Asia). That's just what you'd expect from the historical gene flow patterns, and I'd expect it to apply to Africa as well.
The real question is whether folk notions of ethnicity map onto clusters in gene space. If they do (and they do) it implies different frequency distributions for alleles in the groups. That raises the possibility of statistical group differences. What those differences are remains to be determined.
I'm typing this on an iPad so apologies for mistakes. A picture for you here:
http://infoproc.blogspot.com/2009/06/genetic-clustering-40-years-of-progress.html
Yes, there are clines, but so what? The population fraction in the clinal region between the major groups is tiny.
The distance (e.g. measured by fst) between the continental groups is so large that you would have to stand on your head to not "discover" those as separate clusters.
See also here http://infoproc.blogspot.com/2008/11/human-genetic-variation-fst-and.html
OK, so we just differ in nuances of definition. If you prefer ethnicity to race, that's fine with me.
The usual lame argument is "race doesn't exist, so how could there be group differences" -- but I think neither of us is arguing that side.