It is safe to say that most PhD research areas are in the biomedical sciences. However, this is definitely not a requirement. The timeframe to change your research area will depend largely on what school you attend. Likewise the flexibility of what research areas you can choose from will also vary from school to school.
As an example, here at The University of Chicago, they are quite flexible about what you do your PhD studies in (as an example, a girl in my class is going to do her PhD in public policy). Also, you don't have to choose your curriculum until the end of 2nd year, because you don't actually apply to the graduate program until you are done with the first two years of med school. That said, the sooner you can make up your mind, the better off you will be. Many people here are able to complete all of their graduate course work during the first year of medical school, which allows them to complete their PhD sooner, and alleviates some stress during MS2 and the graduate years. However, it is difficult to do this unless you have some idea what you want to do your research in (it doesn't have to be exact, as there is some overlap between curriculums, and also electives allow flexibility too).
In the UIUC medical scholars program, they are even more flexible than UChicago, in that you can basically do your PhD in whatever you want, so long as you can convince the MSP it will be somewhat related to medicine. They have students doing PhDs in things as extreme as Aerospace Engineering, Electrical Engineering, and Philosophy. Part of the reason they are able to do this is they don't have to answer to the NIH because they aren't MSTP funded. Also at UIUC, generally speaking you will have only completed MS1 before completing your PhD, and you must enroll in the graduate program of your choice at matriculation (because the graduate program provides your stipend).
You will probably not find any program that will let you finish your MD before your PhD, because the risk is too high that the student would just leave after the MD. For most MSTPs, the sequence is usually MS1, MS2, complete PhD, MS3, MS4.
In my own experience of applying, I found that about half of the programs I came across were rather strict about what PhDs were allowed. As a starting point, take a look at my MDApps, because I only applied to programs that were more flexible about this according to each program's website.
