Dear Whitecoat,
I believe applying to a MSTP program (DO/PhD) gives you a better shot at admission than applying to the DO program alone. In contrast, being admitted to the MD/PhD program is significant more difficult than the MD program alone. This is what I heard when I applied: DO schools, especially the ones with graduate schools established within a university system, are seeking to produce research-minded DOs so they really welcome dual-degree students. The source of this information was probably credible, but I don't know if this is totally hearsay or completely true however.
When I was an undergrad, I applied to both MD/PhD and DO/PhD programs. You already know what I ended up doing. For reference, my MCAT was 34 (V-10, P-12, B-12) and GPA 3.6 cum.
I wish you the best of luck.