The reason you can’t see the disk in your Linux installation is that it is being auto-mounted and has access control lists managed by udisks2; no amount of Unix permissions changes are going to give user plex access. The recommended solution is to create a dedicated mount directory and mount the disk to it, as described in this article:
If you want something easier to try first, you can modify the ACLs so that user plex has access to the automatic mount folder for your user. To do this, run the following (change the directory path as necessary):
sudo setfacl -m u:plex:rx /media/user/
You can change “rx” to “rwx” if you’d like user plex to also have write access to the disk.
Out of curiosity, what is the output of running getfacl /media/user/? The command I provided earlier should have granted user plex access to /media/user/ and everything under it. It would not have worked if you ran setfacl with each sub-directory. It needs to be run against /media/user.
But, to Chuck’s point (and as I suggested above), it is recommended that you create a dedicated mount point for the disk following the instructions in the guide provided. The shortcut I suggested is just a way to give user plex blanket access to everything under your auto-mount directory (/media/user/).
Following the guide, what directory did you create you mount points in? That command only affects permissions for /media/username, and only when using ACLs. Using Chuck’s guide, you should be mounting the disk under another location, such as /mnt/ or /disks/.