Agree with the above: every school is different, some schools will have a separate MD/PhD committee, some will send applications discarded by the MD/PhD to the MD only committee. With regard to that last point, it is cold comfort because: 1) the "sending" usually happens very late in the MD cycle (late Jan-early Feb) when garnering an interview invite is difficult and 2) the MD-only adcom figures you'll turn down an MD-only offer if you get a MD/PhD offer and what's the point of being the applicant's "safety"?
Most schools are going to consider 1) are you a good candidate for the PhD with a high likelihood of success in your academic and research endeavors in grad school and career aspirations that will make the most of the PhD, 2) are your research interests and current skills a good fit with one or more investigators/labs at this institution and 3) do you have adequate exposure/experience in clinical settings and can you clearly describe your motivation for a clinical career as well as a research career? If you don't pass through questions 1 and 2 there isn't much point to question 3. The PhD folks are the best judges of 1 and 2 so if I were Queen, I'd have the first pass made by the PhD folks for the sake of efficiency.
Curiously, there are applicants who have little or no clinical experience coming into a MD/PhD program. They are all about the lab and the PhD folks think that they are great. To their dismay and surprise, when some of these students get to the clinical educational activities they discover they LOVE clinic and don't ever want to go back to the lab. So, a continued desire for a lab career after having been exposed to clinical settings is pretty important in choosing candidates who won't jump ship when they discover how much they love what they'd never been exposed to earlier.
