I really don't think that MD/PhD vs. MSTP matters; what matters is your individual residency application and how qualified you are. I would venture to say that no residency program would take a less-qualified applicant from a MSTP over a more qualified applicant from a regular MD/PhD program (non-MSTP status). If you have heard stories about MSTPers being shown special treatment over regular MD/PhDers during interviews I would say that is simply b/c they happened to be the most qualified.
I wouldn't sweat too much about getting into a residency at this stage in the game. If you look at the places listed (e.g. IM at BWH, peds at CHOP) it's pretty obvious MD/PhDers are getting into their first choice, especially in the less competitive specialities like IM, peds, path. That may be less true for super competetive things like derm, rad-onc, etc. but I still doubt you'll have trouble matching at one of your top choices, if not the top choice. Just go to a good MD/PhD program (MSTP or not) with a good group of students, good program leadership, good research opportunities, a proven track record of producing successful graduates, and most importantly - somewhere you want to be for 8 years.