They both insist on their own systems and both are wrong.
As far as I can tell plex only wants separate folders for different kinds of media and file names that give at least some clue to what it is. Plex is much more lax.
It's astounding how much every single system out there fights and fights and fights against showing you your directories, as they are.
I started but didn't finish a Rygel + local-search (nee Tracker) plugin to try to finally get that. I wish the upnp media services were better. I keep telling myself I'll build a nice client/controller... Some day.
Is there anything around that does _not_ force a management system? I really just want a thing that primarily just tracks if I've seen a particular file, secondarily maybe let me control playback from a different device. Actually figuring out what media those files map to is a distant third.