Apply to both, there is no official bias against you for this. The only problem (and it's largely theoretical) would be if the MSTP held your app. until the end, decided against you, and it was then too late for MD admissions consideration. Very remote, but I know it has happened.
Your MS will help in that you should get up to speed quicker in a lab. You'll get one year of grad classes "forgiven" at most schools anyway, so it won't do much more for you. What will make your PhD quicker is getting your reqs done as early as you can, finding your thesis lab and getting going. If you then actually show up and WORK at it, you can usually get out quickly (no 3 hour grad student style lunches/gym breaks etc. - note: this is a generalization/stereotype, so please don't flame with "grad students work hard" posts... I'm just making a point).
P