Great job, fguy!
As I have non-ext3 version as well, your workaround is very helpfull. I made quick test with two mkv files and it seems to work flawlessly. The only thing I've changed is replacing tail command with head, as when you grep config file, AUDIO_OUT variable is in the first line.
I don't think AV sync and mov issues are related to AUDIO options. I will let you know if I experience this.
Anyway, mov file format is not very popular nowadays (I haven't got any), so I wouldn't care so much.
One more thing. Why did you apply dos2unix command in the last script?