More than two months passed and no one confirmed that such thing is possible, so I believe I can safely pronounce this statement:
MeGUI does not support more than one audio track in iPhone (iPod Touch) video.
MeGUI does not support subtitles in iPhone (iPod Touch) video.
The reason I write this is to help others save time. I have spent two whole days trying all possible things to make it work, because I have not found any such statement anywhere on the internet.
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