I prefer to keep lossless audio when I can, but higher bits-per-sample and (usually) higher sample rate yields zero benefit outside of higher sales. I prefer to keep FLAC because the files are typically smaller than DTS-MA or Dolby THD, and are well supported on PCs. Still trying to get Kodi to work with them, but that's for another time
.EDIT: I had taken a look at the Advanced Usage forum threads "On the fly audio conversion" and "Audio Conversion" as well as other posts found with a search for "down16" (a command-line parameter used by eac3to, though I understand that MakeMKV uses ffmpeg, however I am not familiar with how to change ffmpeg's parameters in MakeMKV).
