In my opinion academic programs do favor MD/PhD (just see this year's match results); these programs include Vanderbilt, UMichigan, UCSF, Harvard, etc. If you have an excellent track record in research, with publications, it is more likely that such programs may be able to overlook a lower than average board score, because such programs are looking for future academic "leaders" and they believe prior research experience increases the likelihood that you will remain in academics. Once you get an interview, the field is probably level once again. I would suggest you consider taking Step II to increase the chance of getting the interview and making that first cut.