Plug-ins on volume root.

Im trying to change my setup from SSD OS drive in two partitions, to a recommended division between the OS and Plug-in data drives. But some of the Plug-ins (plex, couchpotato) will only let me choose a volumeroot as the destination. So now i have Plug-in folders mixed in with my media folders. This makes my filemanegment OCD go crazy!! Is this just the way people do it or is there a better way?