Andrew,
For the addition of "cin_quality=1" in the attached format files of mjpg.qt, mp4.qt and flv.flv, I have rendered before and after and the rendered results/file sizes are EXACTLY THE SAME. Have I done something wrong? It looks like that is already the default and does not need to be added to the files.
I just checked into GIT, your revised "dnxhd.qt" file which is really helpful to see what is legal while in the render menu. I will checkin the new "mjpeg.avi" file (you attached here) which I have tested (after I figure something out first).