I agree that it is ranked 5th in predictive value. However, for non "Highly Competitive Specialties" it is not ranked suggesting it is MORE important for competitive specialties.
The OR indicates that "all other things being equal," having a PhD increases your odds by nearly a factor of three. Merely looking at the percentage of PhDs who match and did not match does not say anything except that for a PhD the other factors played a major role in that decision. E.g. for your previous example, Orthopaedics, 3.5% of matched and 3.9% of unmatched had a PhD. I'll argue this difference is negligable. However the Step I of matched was 246 and unmatched was 211; which is likely a significant difference since the 25th percentile of matched is higher than the 75th percentile of unmatched. While both are >201 (which increases O.R. for matching) those who matched are >235 (which further increases the O.R. for matching). So for PhDs, their odds are equal, but say one PhD has a 211 and another a 236, the 236 has a higher O.R.
The statistics are there so you don't have to make assumptions and imply things.