I don't think either iFlicks or subtler demux the video streams (I could be wrong though). I just use those programs on my mac to tag and add subtitles to movies I ripped with makeMKV and convert everything into an m4v/mp4 container file which appleTV knows how to handle. It doesn't take long (1.5 minutes approximately). Same for 3D SBS movies, so I presume no demuxing is taking place. If they are demuxing, the programs take care of it themselves. I don't see any changes in the final video quality of the MP4/M4V.
Where do you post updates?
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