The only potential issue is if the Client is underpowered and can't play the original file format without stuttering or other artefacts. In that case, the Client would need the MC Server to convert the format and stream it to the Client. For example, if the Client can't play high bitrate FLAC files, but can play MP3s, then conversion to MP3 would be required and would be set under Client Options.
Otherwise, playing the original file directly should give you the best quality audio. After all, a conversion can't improve the audio quality of a file.