I am applying to AOA and dually-accredited programs. I have no desire to bite my nails over more than one match; in addition, I am applying IM/EM and also IM. IM/EM doesn't have many programs, so my chances are better in an AOA program. I have been interviewed by MDs and DOs, and have worked with many MDs throughout my education. There is no bias from the majority of physicians. All they care about is whether you are competent, know your stuff, are interested in learning, and whether they can trust you and teach you.
I think whether you run into problems depends on what you want to do. Is it hard to do a ROAD specialty as a DO in the ACGME match? Sure. It's also hard to do a ROAD specialty as an MD student in the ACGME match. But if you're a great applicant no one will care with a few notable exceptions which may change by the time you are ready for match. To my knowledge, everyone in my class who applied to both types of programs is having no problems getting interviews at a wide variety of places they applied.
More than stressing about DO in an ACGME match I would take more time to figure out which residency programs are malignant and avoid them like the plague. Yes, there are residencies out there that are worse than not matching at all. Do your research.