Enable the DLNA server in Plex Media Server to stream music in FLAC format without conversion. That should work for your Yamaha and other devices that support the FLAC format and have a compatible DLNA client.
The Plex Android/Android TV apps convert FLAC to PCM. Unsure if this happens for other Plex apps. See this thread for additional information:
Use Plex app on iOS to control PMP on MacBook Pro (see Plex Companion).
For music, audio will be converted to PCM. However, since PCM is lossless, there should be negligible quality loss for the FLAC files. I believe the PCM will be at 48kHz/16bit, so any hi-res files (96/24, etc) will be downsampled.
You’ll need to configure PMP to send audio to the receiver, not the Macbook speakers. See this post for help with that (the post is about 7.1 audio for movies, but will work for music as well).
Pulled out my old iPad2 (which I thought was too old for this) and loaded up the current Plex iOS app, v5.12.1 (iPad2 running iOS 9.3.5).
It direct plays FLAC music files. I can use AirPlay to play the audio on my Denon 4300H. Plex still shows direct play. The Denon says it is receiving PCM 2.0.
So, it seems you can direct play FLAC audio. It will be converted to PCM, but there should be minimal or no quality loss.
and it seems to be exactly what I need, It picks up all the files from the Plex Server and has a very nice layout and streams FLAC direct to the amp (not airplay)
also it has the ability to search through all the folders and songs