Identifying BME as your program interest will neither help nor hinder you. In recent years there has been an increase in the number of individuals iinterested in BME. I am not sure why this is happening, except for the gee-whiz appeal of BME. Most MD/PhD programs select students without regard to doctoral program interest. The idea is to select the best available talent. No matter what you select as your interest, you have to have outstanding research experience to be competitive.
Admissions committees realize that as a rule, it is harder to pull a 4.0 in electrical engineering than in Biology, so there is some adjustment made for that. But a 2.9 EE GPA will kill your candidacy just as efficiently as a 2.9 Biology GPA. One other thing about undergraduate work, if you want to do a PhD in BME, you must have taken appropriate undergraduate courses to prepare yourself to do the doctoral work. If you were a biology major and your undergrad curriculum was light on math, computer science, engineering, etc., it will be hard to convince a BME program to take you. Because of time constraints (and because MD/PhD students are expensive to feed and care for) programs are not wild about students having to take a lot of undergrad courses to get up to speed for the PhD.
You should contact the schools you are interested in and ask them about the specifics of their BME programs. Questions you might ask are:
What is the relationship between the MSTP and BME? Is it formal, or informal? Formal is probably better because everything is spelled out, and there is less chance of an unpleasant surprise down the road.
What are the course requirements for BME MD/PhD students?
Do I need to take the GRE? (Some BMEs require this of MD/PhD students.)
How are BME applicants evaluated? Is there a quota for BME applicants?
On average, how many individuals interested in BME apply? Are interviewed? Are accepted? Enroll?
Good luck with your application.