Another possibly silly question for me, but does applying to additional programs at the same school lower your chances of getting into the regular md program at all if you are applying to both? As in they do not feel you are a good fit for that particular program (rural medicine, etc) and therefore aren't accepted to it, do they lower your chances of getting into the MD program at the school😕
I'll answer from the MSTP perspective as that's what I'm most familiar with.
The short answer is: in general YES. And here's why:
1) MSTP generally require tons of research. And by tons I mean one year minimum (~20 hours per week). Even that is the bare minimum. The reason is that MSTPs don't give much weight to stuff like volunteering or clinical exposure etc. You are expected to have at least done some but 20 hours vs. 50 hours vs. 100 hours don't make a hell of a lot of difference. So the priorities are different. If you focus on research, then you may lag behind on the stuff that are important for the MD-only applicants.
2) Some schools require you to choose MSTP or regular MD (Penn comes to mind). You are evaluated for one or the other and once past the deadline, there's no switching. There's also no going to the other side if you are rejected.
3) For the nice schools that give you the option to switch to MD-only, it only happens AFTER you are rejected from MSTP. That means in some cases the MD committee won't even get to look at your application until you are rejected. Now if you consider the fact that MD/PhD admissions process is typically later in the season compared to MD, you are now at a serious disadvantage at rolling schools, particularly ones that admit a large portion of their students early (like Michigan). Also, some MSTPs have a habit of putting some students on hold for months at a time before making a decision, so you might be rejected starting september through january by which time even if you got an interview with MD-only, you may interview only for waitlist spots.
#3 may be mitigated if you are invited to interview with MSTP but were rejected post-interview. Many places do both MSTP and MD interviews together so that if MSTP rejects you, the MD get to make their decision immediately. But if you are invited for MSTP interviews, then you are obviously a strong applicant and should not have trouble getting in somewhere.
Finally, while I'm not as familiar with PRIME, I seem to recall that the PRIME admissions process have little impact on the regular MD admissions. In fact you must have gotten into med school first before PRIME accepts you, or at the very least it's concurrent. Plus, aren't the stuff that you may do for PRIME very much overlapping with stuff that a regular MD applicant may do anyway?