There are four types of programs.
1) Consider you for MD and MD/PhD separately. At these schools you interview for both programs when you visit and it is possible to hold both types of acceptances at this type of school at the same time. The two schools that come to mind are Baylor and UMich, but I am certain that there are more.
2) Consider you for MD first, then consider you for MD/PhD. A couple schools require the MD program to certify you before you can get a MD/PhD acceptance. You interview for both programs when you visit if you get a MD/PhD interview. Some that come to mind are UCSF and URochester.
3) Consider you for MD/PhD and then DO NOT consider you for the MD program. The only school that explicitly states that they do this is UChicago. However, I am certain that some other schools are also doing this or else only push students back to MD in rare cases (Hopkins, UPenn?).
4) Consider you for the MD/PhD and then consider you for the MD program if you are waitlisted or rejected. Typically, you will interview for both when you visit if you obtain a MD/PhD interview. At some schools it is more likely that you will be considered for MD if you are waitlisted/rejected post-interview. At other schools, it is likely that you could be considered for MD even if you are rejected pre-interview for MD/PhD. This catagory in one way or another comprises most MD/PhD programs.
I think one could easily argue that waiting for an MD/PhD decision could hamper your MD chances. At some schools this is true, at others it is not. For example, I was accepted to Duke's MD program after being waitlisted by their MD/PhD program. I was accepted to both Baylor and UMich's MD programs, but they have the separate MD and PhD processes.
I hope that answers your question. You know I think that you have a very strong application for MD/PhD, and you shouldn't let any fear of not getting in stop you from applying that way.
Good luck!