Per my article - Did You Know? How ostree update merges changes into etc and var - /usr/etc contains the version specific golden copy. I see a 0 byte file at /usr/etc/hostname when booted with 41.20250309.1 (bluefin-dx-nvidia:stable).
Based on what I learned while putting the article together I would not expect /etc/hostname to be touched if it has been modified.
Try resetting the hostname (using hostnamectl) and then switch back. It should not be touched.