Hi,
My impression is that most schools want most of their students to work in a wet-lab/bench setting. Some do not even allow any other option.
The more enlightened (or well funded and so can afford the daliance 😉 ) programs that allow students to pursue PhDs in "non-traditional" areas will still most often advise against or even prohibit working in a strictly clinical realm. Their reasoning is that you'll have plenty of time in clinics and that the PhD should be a time to acquire a different skill set.
There is a very recent trend, with which I strongly agree, to emphasize clinical research in a few programs (the Case Western Reserve University SOM/Cleveland Clinic effort to train MDs in clinical research is a notable and perhaps the most formalized one to date). However, these are not yet MD/PhD programs but rather an extra year in which one is trained in clinical research. This may change, but I believe it to be the current situation.
Now, if anyone has a more up to date info set or a different take on things, I would be very much interested in a reply. While the typical MSTP has its place, I think the current level of training/understanding of clinical research is what is leading to the current quality thereof (more simply, clinical research is in need of more rigor). That should happen in med school, certainly in all of our general education and also perhaps as a separate masters level track. I don't know enough to recommend for or against a clinical science PhD, but it strikes me that the MD should be just that.
Best,
P