While this may be true (dunno statistically), it's VASTLY easier to squeeze into a PhD program at the same school once you get into the MD program. PhD programs in basic biological sciences have substantially decreased in competitiveness and perceived attractiveness in the last 10 years that even the top programs essentially have no leverage in the admission process.
Meanwhile, applying separately to PhD programs exposes you to the scrutiny of basic scientists of your career trajectory if your CV sounds more like an MD's CV. So my advice is: apply to MSTPs, and as a backup apply to MDs.