I'm assuming you installed the real Calibre via the Calibre web site using the "isolated" install:
wget -nv -O-
https://download.calibre-ebook.com/linux-installer.sh | sh /dev/stdin install_dir=~/calibre-bin isolated=y
and not the flatpak. Thanks. That's good to know. I'll add that to my bug reports on Bazzite's github page and the Calibre flatpak's github page.
EDIT: After re-reading your post, now I wondering if my assumption was wrong and you installed the flatpak. If so, I'm really worried. When I first ran into this problem, I even un-installed the flatpak and re-installed it. Same problem.