As jonathanm asked, what instructions are you referring to?
If you only map folders on disk1 to the Plex docker container, then quite predictably only media in those folders on disk1 will be available to Plex. If your media is spread out over more disks, then it is not strange at all that half of your library is missing from Plex...
I can't see any reason not to map the media shares through user shares. Just don't confuse "/mnt/user" with "/usr", the latter is off limits :-)
Previously I just assumed that you referred to Tools, New Permissions, but not I'm not so sure anymore. How did you try to "redo permissions"?
I followed the examples here:
http://lime-technology.com/forum/index.php?topic=24321.0
The one I used was: sudo chmod 755 -R "<plex media directory>"