Let me get this one since I have crappy undergraduate grades and just been through the whole application process. OMFS residencies look at your overall undergraduate GPA, most of them do not break it down into pre-dental prereqs or science GPAs. In my experience, those M.D. integrated OMFS programs that involve high competitive medical schools (Harvard, Mayo, Michigan, and many others) will look more closely at your undergraduate GPA because of the medical school's requirement for admission.
What's interesting is that according to an article survey in the Journal of Oral & Maxillofacial Surgery, the 4-year residency programs actually look closer at the undergraduate grades!
Regardless whether 4-year or MD programs look closer at your undergraduate grades, if it is low (below a 3.0) like mine, then your chances of getting an interview will be compromised. If you kicked @ss on the Part 1 boards, lets say a 95+, I believe your undergrad grades may be over looked, but maybe not at a prestigious medical school. Again, these prestigious medical schools has their own minimal cutoff for interview selection (often than not, these OMFS residency programs, the medical school has a influential vote whether to accept the applicant or not).
Remember, some M.D. OMFS residencies has more say who they want to accept, but some M.D. OMFS residencies have to listen to the medical school admissions office on who they can accept.