Hi David,
I have to check this, but I did some OMF/AAF export tests with Automatick Duck, and it appears to me that the problem you describes only happens when you “Break Apart” clip elements.
If you only detach audio from your clip, then the channel configuration is still ok, even if you delete video.
But you’ve got to manage your channels with “open in timeline” function, which sometimes can be annoying. I work in Dual Mono and sometimes I wish I could “open in context of my project” instead of opening another timeline.
Otherwise, another workaround I often forget and that BenB reminded me, is that you can connect your video clip below primary storyline. It then acts like an audio clip (if there’s video on your primary storyline). And exports fine in OMF.