Maybe I misunderstand how BD authoring works, but couldn't you create 21 playlists, each with the main video and a single audio track and just select the desired playlist (ie audio track) from a list of 21 links to the individual playlists?

I'm assuming that subtitles can be selected from a separate menu at the beginning without having to have a huge matrix of audio/subtitle combinations.

I too have noticed that some players handle media files differently from official Bluray or DVD structure, so the quality of mkv can not be guaranteed. This need not be a deterrent since mkv can be converted into simple Bluray structure and burnt to a disc to appear like a real Bluray disc. Of course there is still the issue of having to select audio/subtitles through the player instead of a proper menu, but my suggestion still stands of including a static introduction presenting the menu of subtitle and audio options to facilitate selecting the number of the desired value through the player and then going forward or back a chapter to restart at the beginning of the movie proper.