If you're not accepted to an MD/PhD, you can only be transferred to MD admissions, not PhD (and some schools won't even transfer you to MD; it depends on the program). So as ClimbsRox implied, you'd have to apply to PhD programs separately. Most programs have late December deadlines, but you'd have to kind of be on top of the ball to apply to PhD programs if it seems the MD/PhD thing isn't going to come through.
I received 2 MD interviews after being rejected for the MD/PhD at those schools, but I agree that as a whole it puts you at a disadvantage time-wise.