With the MOV H264 codec you use to be able to do multichannel exports with any number of mono tracks. Now that you got rid of that, there's no way to make lo quality proxies with multichannels. I mean you have the H264 in and MP4 but you can only export mono, stereo. or 5.1. Why can't you just let the user choose the audio configuration. I would like to have a full stereo mix and an M&E stereo mix on a proxy. The audio config options for the H264 MP4 codec are really limiting.
Antoine (Autokroma.com) commented
I added that feature in AfterCodecs ! https://autokroma.com/AfterCodecs/
As a bonus, if it is for preview, you can use Speed=8 which is way faster than Adobe H264