@ Guntmeister:
Thanks for the reply! Allthough I was not able to get it working with MP4Muxer I somehow got an Idea what to look out for after digging a little more into the issue.
Out of nowhere I got the idea that this might be possible by editing TAGs and to my surprise
MP3Tag does the job for *.m4v and *.mp4... For everything else it seems that there's going to be a LOT of converting going on in the next few weeks ( after some more investigation on specific filetypes )