I dunno. I guess it's program and specialty dependent. I worked in research at a top hospital and saw first hand what happens to people rotating through. Yes, they get letters and they get outstanding experience, but the ones that matched to the program didn't do so because of their away rotations. I spoke to the fellows about it, and one very involved fellow who is now an attending there said that she did not know of any resident ever matching to the program without pedigree and connections, and that away rotations had nothing to do with it and that no one really cared about the away rotations. And these are people from top 10 MD schools with outstanding research and ridiculous academic background (undergrad and MD from top 10 schools, etc.). They did their 3rd year rotations at hospitals like MGH, the Brigham, Barnes, UPenn, etc., and they came prepared to dominate. If you do an away rotation at a program like that, it's far more likely that you are going to hurt yourself and not impress anyone. They're already going to have a bias against you and every minor error you make is going to be magnified through their biased lenses. From what several PDs and residents/fellows at several top programs have told me, I can safely say that in top programs, doing an away rotation does not really count as a "connection".
As for doing a research year, I know of several people applying to Ophtho as DOs (and also MDs) who did not match the first time around because they did not have any real networking in the field. Second time around they did a research year and built their connections and when it came time, they matched at the programs where influential people they worked with called/wrote outstanding letters and truly vouched for them. Go ask in the subspecialty forums and see what people say. If this kind of thing happens even in mid-tier and low-tier programs in competitive specialties, it's not an extreme thing to immediately assume that DOs who match at top places had great people calling/writing letters for them.
If a program has a filter to cut out all DO applicants, it's unfortunate but I completely understand why they are doing that. If you were a PD at a top program, you'd probably do the same. I also completely agree with you that the bias at many top programs will never be fixed no matter what kind of connections someone has. There is an ophthalmologist (huge name in research) that, prior to becoming an ophthalmologist, was an optometrist and PhD. He was already a big name in research and did work at MEEI/Schepens. He went to CCOM later on while his research career was soaring, and when it came time for residency, MEEI didn't take him. Obviously his research and connections at MEEI was ridiculous - he was basically an experienced researcher there. I'm not sure of the details, but he did an ACGME ophtho residency elsewhere. Let that sink in.