Here's what happens... thousands of applications pour in for admission to the MD program beginning in July until the application deadline in mid-autumn. Those applications are reviewed and invitations for interview are issued (or applicants are queued to receive an interview invitation later in the season) starting in August -- sometimes earlier. Meanwhile, a few hundred applications for MD/PhD come into a different bucket and are reviewed with some applicants offered interviews and others shunted, eventually, to the MD admissions bucket. By the time a decision has been made not to offer you a MD/PhD interview, it may be October, or later. That means that most of the interviews for MD slots have already been allocated to people who applied to MD-only. There is also the idea that if you really want MD/PhD and you get that offer elsewhere that you will prefer it to an MD only offer so why should the school waste an interview on someone who is unlikely to matriculate unless it is the only offer.
I've no advice per se but I just want to offer an explanation as to why it decreases your chances of MD only at the same school.
