Your template settings are wrong. You've got the appdata path or /config path going to a host path of /config/Library/Applications Support/Plex Media Server
This location is in RAM and will be lost at every reboot. The entries for /config are automatically adjusted by the system to reflect the base path of whatever you have set in Settings - Docker, Default appdata path, so it would appear that you've gone to show more settings and manually changed it yourself. This should be something akin to /mnt/user/appdata/Plex
Also, for your /transcode path you want to set this to be a subdirectory off of /tmp (ie: /tmp/transcode or /tmp/plex etc) Doing it that way you have it (currently mapped to /tmp), Plex has full control over that directory, and if it decides to delete stuff in it (which it does) that was placed there by the OS, weird problems will results across the entire GUI