I get the same results from MD, MIDI Tool Box and recently acquired Animoog.
What I see in all apps are the other DIN and USB jacks but not the actual jack my iOS device is connected to.
What I discovered is the physical jack that my iOS device is connected to is actually connected to the app behind the scenes. In MD I would then select DIN 1 for the out if I wanted to Route MD to DIN 1.
Is that how MD is suppose to work? My other two apps are working the same.
im starting to believe it's an iOS 10 issue.