You convert to FLAC because:
1.) There are currently no software decoders out there that will play TrueHD/DTS-HD Master properly.
2.) Size of the audio track is considerably smaller after converting, yet still maintaining a lossless track.
If you are using a Popcorn Hour or have a HTPC capable of bitstreaming you could likely leave the audio track as is, but since I have neither I have never tried it.
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