Unraid 6.11.5
Nearly the same here: the .ssh directory is a symlink to the USB stick where (/boot).
I tried to adapt the needed right on files like ssh wants it - no chance: chmod is not working on USB stick (somehow protected?)
So I decided to delete the symlink an d rsync everything to the user (root) .ssh directory - adapted the file-rights according to ssh needs and that works for me by now.
I do not really like to cut that link but otherwise I can not log in with the key.
Might it be that "My Servers" plugin is the roor cause? At least I saw that "My Servers" changed the config file