Just tested it (GNU coreutils 9.8 on nixos, root on zfs) and .. still exists in /, but seems to be the same as .

Is it bottom layer in wayland terminology (the one for bars and stuff)? In that case I think gtk4-layer-shell is the answer.

You could give the home partition two keys, one stored on the root as you described and the other stored somwhere else/remembered.

Check out ntify, it might fit your use case