During 4th year, as a DO student, you can enter the DO match, the MD match or both additionally you can enter the Military match if you are on an HPSP scholarship. There is also the San Francisco match which I am not familiar enough with to comment here.
I believe this list the MD or DO column merely denotes whether it is an AMA or AOA residency.
Many DO students enter the MD match as evidenced by at least 50% of the students on the Midwestern page having MD residencies.
The overwhelming opinion of DO students is that there should be a combined match instead of separate AOA and AMA matches. The AMA supports this, but the stubborn old guard of the AOA does not.
The way it is set up now, if you do both AOA and AMA matches and you match to ANY spot on your AOA list regardless if it is your 10th choice, you MUST do that residency even if you matched to your #1 or #2 choice in the AMA match. This strong-handed policy is why many DO students each year do not even enter the AOA match, even if their 1st or 2nd choice would have been an AOA residency spot. As such, many DO students are scared away from potential DO residencies for fear of going somewhere they don't want to and many DO residencies sit un-used every year.