Hey Robin sounds like a great workflow and I do have some advice for you:
You’re on the right track with creating separate .stream files with each referencing a different audio pid. And then use that info in the alternative tracks article to tie them all together for playback.
The article shows how to use a separate startup smil file to make sure all streams start at the same time.
If the audio is already the right format then there’s probably no need to transcode.
unless you want different video renditions.
As far as Engine: Transcode multiple audio channels and split each stereo pair (left/right) into two mono channels.
Looks like it can be done on the encode side of the transcoder. Two encodes, one for left & one for right.
You can see this post for reference:
If you still need a hand, please feel free to submit a support ticket to us and the engineers can walk you through it.