As for your question on audio, I don't know the exact procedure, however I assume you keep the same structure for all files - for example:

.M2TS structure:

Track 1: Video
Track 2: Audio A
Track 3: Audio B
Track 4: Audio C
Track 5: Audio D

And then flag which tracks are available to the .mpls using the .cpli, however exactly how to do that I have no idea. The only other thing I would say is that I would also assume you need your codec and encoding settings to be constant throughout. That is to say while there's nothing stopping you from going from AVC 1080p to MPEG2 480i mid-movie that kind of change would undoubtedly cause a less seamless playback, and even going from the same codec to a different profile or other changes within the encoding settings might cause a delay in playback also.