Many schools have things set up so that during interviews, one or two interviewers will be evaluating you specifically for the MD program. However, schools vary on what they do specifically after that point. In my personal experience, many schools will hold off on evaluating you for MD-only admission if you are waitlisted or on hold with the MD/PhD program. If you don't find out that you have been rejected until later in the cycle, chances are that more of the MD-only spots will have already been filled by the time the MD-only committee can really review you in detail and/or offer you a spot.
On the other hand, if you are denied an MD/PhD interview early on, many schools will evaluate you for an MD-only interview and your chances at admission may be a little bit better.
Again, this isn't the case everywhere, but I have found it to be true of several schools.
I know that this isn't exactly what you were asking, but I feel that it's important to say that even if a school considers MD/PhD applicants for MD-only admission, the process deviates a bit (sometimes negatively) from the normal MD-only review.