This should only be the case for the Plex Updater Service.exe process
The rest of the Plex Media Server processes should still be using the LocalAppDataPath specified in the registry
The updater service runs under SYSTEM and allowing users to specifiy a path for the logs for it introduced a security vulnerability - so it is now fixed writing to the %LocalAppData% for SYSTEM
I would expect you to be running the Plex Service under a different user than SYSTEM. It is very unwise to run it as SYSTEM.
Yes we do now clear the LocalAppDataPath in the registry for user SYSTEM as part of the fix for the security vulnerability (See Plex Media Server - #586 by janoskk)
