I honestly don't know about what they'll be doing about rejections. I assume they'll keep a few lingering around just in case they lose a few to waitlists, but frankly since most that are eligible, i.e. accepted already to med school, will have given up their slot in favor of a sure acceptance at another MSTProgram, I don't know how likely it is that anyone else will come off. I got lucky in that I didn't have to deal with hanging on to MD only past May 15 in hopes of MSTP since I was waitlisted by MD until after the deadline.
In any case, yes, Stanford is the only place for me for a number of reasons (spouse, research, etc.), so I'll definitely be staying here. Are you still on the MD waitlist? Accepted MD, waiting MSTP? Stanford certainly has some fantastic opportunities, so I wish you the best of luck.