So when you acces plex via a web browser and read a FLAC music file, it actually transcode flac to mp3.
It is because (at the time) browsers (firefox/chrome/IE) didn’t support FLAC natively.
Windows 10 is now supporting FLAC natively and most browsers (firefox/chrome/edge) have integrated native FLAC support.
I think it should be time to enable directplay of those flac files now 
Edit:
It was already asked years ago but at the time it was about creating a plugin to enable such support==> https://forums.plex.tv/discussion/127691/prevent-plex-web-from-transcoding-flac-to-mp3#latest
Should be much more easy to avoid transcoding now with native browsers support.
