First, it will help to call the programs directly and ask them. Don't talk to the secretary or the "coordinator" but go straight to the big cahuna and say, "Hi, I'm a D.O. student interested in applying to your residency program. As you know, osteopathic students are required to pass the osteopathic licensing exam---called the COMLEX---given by the NBOME, but also have the option of taking the USMLE too. Although it is an added expense and time commitment, I'd like to know if your program prefers that osteopathic students have both USMLE and COMLEX scores or will just the COMLEX suffice?" Some will say both others will say just the COMLEX is fine.
Since there is so much regional variability as to which programs are familiar with the COMLEX and which are not, my advice is to bite the bullet and take both Steps 1 and 2 of the USMLE during medical school. They mirror the COMLEX closely and since you're preparing for one set, it won't hurt to take the other. No one will care about which step 3 you take and taking step 3 of the USMLE is beyond redundant if you're a D.O. as the COMLEX is accepted in all 50 states now.
Bottom line: It will help at certain ACGME programs to have USMLE scores, not because program directors are biased or anti-D.O. or anything like that, but just because of certain bureaucratic paper-pushing issues. Maybe 15 years from now the process will be more "bilingual" when it comes to USMLE and COMLEX scores. Until then it pays to have both. Relatedly, by taking both you can imagine that you're doing those behind you a favor. As programs become more familiar with the COMLEX and are able to directly compare USMLE and COMLEX scores within individual applicants, they will be able to generalize to future applicants who only have COMLEX scores. If that doesn't make you feel warm and fuzzy about the whole process, nothing will.