It's their loss then because they are missing out on strong, competitive applicants by emphasizing DO preferences.
This may change in the coming years. I think what happens after 2020 will be different from present trends.
You're right that some DO applicants are strong, but MD applicants who go unmatched are just as strong, if not stronger. The issue with competitive specialties is there are more applicants than seats available. So unmatched applicants are competitive but for whatever reason went unmatched. It's not like unmatched MD applicants had red flags in their applications that make them weaker than DO applicants. With former AOA programs now becoming ACGME, they offer more openings for possibly unmatched MD applicants to apply to and pursue their specialty of choice.
MD schools are backed with strong research and networking opportunities. DO schools don't have these resources. If DO students continue to match into ACGME residencies after the merger, the likely contributing factor is continued DO preferences by former AOA PDs, which again is their loss.
I'm not saying these specialties will become inaccessible to DO students after the merger, but it's just extremely unlikely. It's not at all easy for DO candidates to outcompete MD candidates backed by strong research and networking backgrounds, and this is due to the fundamental limitations of DO schools.