my smart TV app (samsung UE55F8000) doesn't render non-latin subtitles correctly
I am assuming this is from your experience, and not a "published feature" ;-)
If you haven't already tried it, Subler is a utility designed specifically for adding subtitles, however it will losslessly convert the mkv wrapper into an mp4. It will not only rewrap, and not transcode, the video to an iOS/iTunes friendly format, it will transcode the audio from ACC to AAC if necessary, and it will optimize the location of the mpeg-4 atom in the resulting file for iTunes friendly use. It uses a friendly drag and drop paradigm. Download Subler, unzip into your Applications folder and launch Subler. Type command-n to begin, and drag your mkv file into the window, as well as your subtitles file, and choose from the simple available options. These will not be hardcoded subtitles, but perhaps having a properly soft-coded subtitled mp4 will allow your non-latin subtitles to appear without hard-coding them. Again, it does not transcode video, only audio.