Many in the committee weighing applications at various MD PhD programs are likely to be nonEnglish speakers with their own sore spot about MCAT VR, though it is true that MD PhD programs get their academic picks. Two science 12s are very strong, though, so there will be competing applicants with higher composite and lower science scores.
So much of MD PhD selection has to do with predilections of the admissions committee and research interests I suspect. These are people looking for others who will work with them in the lab. Start reading novels and poems and tell people in the interview that your low VR score was a wake up call. It is an odd thing to be able to interpret biological science passages so well yet have messed up the VR so badly, because there many biological sciences passages that require the same kind of fixity of consciousness.
If I were you I might do another review of the sciences and try imagining you can actually picture the author of VR passages as a person and use your normal social instinct for communication to understand what they are saying in a straightforward way. I have a feeling you are using some kind of underlining system or other MCAT prep nonsense that is distancing you from the expressive and appelative dimensions of what you are reading. To score that low you aren't reading VR passages in a critical way so you don't have the shared understanding of the author's intention the test maker presupposes in intelligent reading. Picture a kind of sexy bookish lady with horn-rimmed glasses or an avuncular genius who is an old friend though trying to get across something outside your normal field of comfort. If you imagine that they will be disappointed as a friend if you don't have something substantive in reply, you will find you understand the questions better.
My feeling is that you might consider retaking the MCAT if you think you can defend the 12s in science, but you can't take those for granted, so it is a difficult question. I would explain the retake of the test in interviews as a point of pride mainly to show you are a good reader.
Also, if your thoughts are so strong to research, you can use the summers in a standard MD to build a resume for a strong fellowship. This can get you to exactly the same place career-wise in research in the same or less years. The MD PhD stipend and tuition waver are good, but they aren't as good as a few years of top shelf earnings at a good teaching hospital. What I mean is that under money practical wisdom imperative the MD PhD isn't really so great compared to alternative pathways. So much of the early MD PhD curriculum is the MD curriculum anyway, so work life isn't all that different either. You could be doing the same thing in ten years either way. With the MD and your own benchtop, ideas, experience, and publications, nobody will care. Learning how to think of research problems, trouble shoot SDS PAGE gels, know when to use Current Protocols or Maniatis, being the one with the right LSC cocktail - National Diagnostics - those are the things a principal investigator really cares about. Whether a PhD dissertation is first in the line of a scientist's research it isn't the end all and be all and doesn't matter that much in all but dysfunctionally farked labs where the PI or some old never ending graduate student is an open sore of personality disorder, which is always a risk anyway. An MD with a curriculum vitae is still a doctor of science.
