Like most things, this is variable.
Many schools will not release waitlist numbers to MD/PhD applicants because there is no reliable way to interpret them. You could be #1 on the waitlist, but that doesn't matter if everyone is keeping their acceptance. Alternately, you could be #10-20 and get in if most people decide they would rather train at another program. I'm sure program directors and some administrators have this data, but most students/applicants are very much in the dark.
To add more complexity, some schools require that applicants be accepted to both the MD/Phd and MD programs independently which may mean that the entire list gets held up if a prime MD/PhD candidate is stuck on the MD waitlist. I think this is becoming less common, but it happened to 2 of my classmates and myself during our application cycle and it was exactly as frustrating as it sounds. I actually accepted an MD-only spot so that I wouldn't be locked into another MD/PhD program with a June 1st start date. Ultimately it worked and I got into my first choice school at the end of June, but it was still a headache.