I don't see where you would think that "MSTP would give you a better chance". They aren't just looking for researchers. They are looking for physicians. Therefore they will be looking for all of the qualities they desire in someone applying to an MD program AND the research skills that can be applied to succeed in a PhD program.
And as far as getting in MD only with an MSTP application, it depends on the school. Some will reject you and immediately consider you MD-only. etc. etc. etc. I would suggest contacting the individual schools.
Also, don't apply MSTP unless you want to be subjected to a long long road. The MD route is long enough.