For many of those programs (with the notable exception of MD/PhD), the application process is the same and you don't even apply to the second degree program until after matriculation. You can express interest during your application cycle if it fits in with your story and what you want to do, but it doesn't really affect your chances.
For MD/PhD, there are much fewer seats available and so competition is intense, but it takes a special kind of person to apply MD/PhD anyway so the group might be self-selecting. Applying MD/PhD may hurt your chances for MD-only admissions at that particular school (if the school considers you for both) if the school only routes your application to MD admissions after you've been rejected from the MD/PhD program. That rejection may come relatively late in the cycle and so the MD committee wouldn't be reviewing your application until then, when there are fewer seats available in the program.
