Track Selection
Plex defaults to the first audio track that matches your language settings. If you select a different track, Plex remembers that selection the next time you play the same file.
You can re-order the tracks and set/change language flags using MKVToolNix or similar tools.
Supported Audio Formats
Support for audio formats varies by Plex client. Unfortunately, there is no master list/matrix of which clients support which formats.
If the client supports an audio format, Plex will try to direct play it (stream it unaltered).
If the client does not support an audio format, Plex will transcode it to a supported format.
Example 1: Plex Web using Chrome on Windows 10.
Chrome supports AAC 2.0 audio. If you play a media file with AAC 2.0 audio, Plex will generally direct play it.
Chrome does not support Dolby Digital (AC3). If you play a media file with AC3 audio, Plex will transcode the audio to a supported format.
Example 2: Nvidia Shield and movie with TrueHD audio.
The Nvidia Shield can passthrough (bitstream) lossless audio formats such as TrueHD and DTS-HD MA.
If the attached audio equipment (receiver/soundbar/etc) supports the format, the Shield will pass it unaltered.
If the attached audio equipment does not support the format, Plex Media Server will transcode it to a supported format.
Real World Example
The Nvidia Shield Pro is the only off the shelf device that supports Dolby Vision, HDR10, and passthrough for TrueHD + Atmos and DTS-HD MA/:X audio.
If your audio equipment supports those formats, the preferred setup is:
Shield ← HDMI → Audio Gear ← HDMI → TV/Projector/etc.
The Shield will direct play the media (stream unaltered). The audio gear will play the selected track and pass the video to the display.
Some TVs block passthrough of TrueHD and/or DTS audio formats, so attaching the Shield to an HDMI input of the TV may not work.
Other scenarios are possible. It depends on your equipment and which video/audio formats you want to support.