I appreciate the thanks -- I almost didn't post because I didn't want to get embroiled in any controversy. But I thought the information was worth having here and I couldn't find a clean reference anywhere else on the net.
I might note that the only trouble I've run into with doing this (demuxing MKV files and remuxing again into a TS container) was that *sometimes* the framerate is incorrectly reported. In that case you need to set the rate in tsMuxer on the video stream. This may be a fault of the MKV format, or perhaps the file wasn't encoded properly in the first place -- I dunno, but the symptom is easy to see (the audio is out of sync on the muxed TS file) and easy to correct.
Like the AVI container, a lot of garbage can be contained in an MKV file -- I'm lucky in that I produce the files myself for the most part so I know what's in them, but in talking with others and the limited experience I have with other folks' MKV files I've seen all kinds of stuff contained (which is another reason I don't think Adobe should provide native support -- it might be a mess trying to deal with that). Still, the approach I outlined should work nearly every time.