My friend did one of these - the program really isn't as homogeneous as it sounds (at least in his case). For the first 2 years (and summers) you're working on your BS in some meaningless degree area that covers the requisites. When you satisfactorily complete that, you automatically gain admission to the medical school for your MD. So, you'd tackle the FAFSA just like people on a longer plan. While you're doing the undergrad part, you're probably a dependent, and an independent while in medical school.
The BS part is separate from the MD part, it's just guaranteed that you'll get in if you do the work in a BS/MD.