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I got to thinking and I was able to fix the issue. Turns out my rclone script is mounting everything using the root user. In the bottom of the mount script I added --uid 99 and bellow that --gid 99. Now the script is mounting everything as the nobody user. Tested it with 6.9.2 and everything worked, upgraded to the beta 6.10.0 rc2 and everything is still working. I still don't understand how how sonarr could write to the share owned by root in version 6.9.2, but not in the beta. Maybe something for the devs to look into but that beyond my knowledge of linux. Hopefully this helps someone in the future.

Update, I was unable to fix the issue. Even chmod 777 /mnt/user/mount and then changing ownership to nobody:users didn't work. For some reason the folders and file past /mnt/user/mount/mergerfs/google-drive/ would still be owned by root, and nothing else could write to it. So I downgraded back to 6.9.2 and then everything started working just fine. Sonarr, radarr, and Readarr are able to write to their perspective directories just fine. Also I should note that Readarr was not affected after I ran the fix perm tool, its base directory is not the same as rclone. The same can be said for SABnzbd, rtorrent, lidarr.

Everything has been working great until I decided to update to the new beta, so that could have something to do with it but not sure. I use unraid with plex and the normal collection of automation programs (sonarr, radarr), and SABnzbd, and rtorrent. Everything was getting an access denied error. I did some googling and saw some responses about using Tools > Docker Safe Perms, and Tools > New Perms. That fixed the issue for all of the shares except for my rclone mount. So rtorrent, and SABnzbd work normaly, but sonarr still can't import the new file into the media directory which resides in the rclone share. Digging into the rclone share it seems that using the tools above are not setting the correct permissions, or users to those directories that reside in rclone. The rclone share looks like /mnt/user/mount/mergerfs/google-drive/media/TV or Movies and then down from there. The folder "media" is owned by nobody, however any deeper than that it is all owned by root. I can't seem to get the permissions, and ownership to trickle all the way down to the folders and individual files within. Any help would be greatly appreciated. Edit: I have also tried using Midnight Commander, and running the command chmod -R u-x,go-rwx,go+u,ugo+X '/mnt/user/mount' and chown -R nobody:users '/mnt/user/mount' in terminal just incase something was timing out. homeserver-diagnostics-20220104-1522.zip