If you are running in docker run: docker exec -it plex bash. For Windows you can download binaries from Releases tab and DIY.
Get into plex installation directory (eg. cd /usr/lib/plexmediaserver).
Run curl https://raw.githubusercontent.com/Saoneth/plex-custom-audio/master/install.sh | sudo bash
To map audio tracks run ./Plex\ Custom\ Audio\ Mapper as plex user (or docker exec plex "/usr/lib/plexmediaplayer/Plex Custom Audio Mapper" on docker)
You can speed up maping process by limiting scaned directories. You can provide them as arguments for mapper. `./Plex\ Custom\ Audio\ Mapper "/Movies/" "/TV Shows/Some very specific movie (2020)/"
Caveats
It remuxes (while playing) everything which has custom audio (even when you select build-in track).
It will require video transcoding for codecs not supported by hls or dash (eg. xvid) when playing from web player.