I'm basically in the same boat as you (very committed to MD-PhD, but see MD only, with the potential to apply for a PhD later, as a back up if I don't get into any strong dual degree programs), and so I'm hoping someone answers this question.
I'm particularly curious in the case of WashU (whose secondary I'm hoping to fire off today). According to their MSTP office, people who put down MSTP-only get only interviews for the dual degree program, while people who say their interested in both MD and MSTP get an additional interview when the visit, with someone from the Med school. That's not particularly surprising, but this is: If you put down both MD and MSTP, the MSTP committee will only start considering you until after the MD people have approved your acceptance to the part of the program. In other words, it seems like if you put down both MD and MSTP, there's an added threshold you need to pass in order for the MSTP committee to consider you. (Not a tremendous threshold, since if you were competitive for MSTP you'd probably get into the Med school as well. But at the very least this system would seem to put a lot of pressure on that one MD-only interview). Am I understanding this all correctly?
So anyone have any advice/experience/hunch regarding this issue of applying to MSTP only or both MD and MSTP?