It seems impossible for Mac OS X users to play 6.1 FLAC audio track. And a lot of windows user cannot either. (You need to confess such format is uncommon. And in Windows 7, ffmpeg is not supported anymore, at least up to now.)
Could you please make a 5.1 AC3 audio track or AAC whatever distinctively that can be played "normally"? You can just upload a new audio file that can be easily merged into the original mkv file. Thus whoever prefer the 6.1 FLAC can play 6.1 in Windows, while other OS users can also play this file.