I might be able to a bit more helpful if there is a specific school or set of schools.
For some schools, you can even apply regular MD and then transfer into the MDPhD program once you're a student.
Here are the schools I applied to:
Columbia
UCLA
Duke
Harvard
Johns Hopkins
Northwestern
Stanfod
UC- San francisco
UC- Davis
Univ. Colorado
Univ. IL
UPenn
UWashington
Cornell
For these, or at least the ones I've gotten secondaries from, you don't apply to the PhD program. Ever.
For some, as I said before, you're considered for the MSTP program. If rejected, you get turfed to the MD Only admissions. For others, your considered for MD first. IF accepted, you get sent to MSTP program.
For the latter, you get an MD acceptence before you are considered for MSTP. For the former, you are considered for MSTP and may be considered after rejection for MD only.