The flatpak is definitely a reasonable option (and more in line with Bazzite's philosophy). I initially had the flatpak version installed, myself. But, since it isn't official, I eventually worked up the nerve to see if the official, isolated install of native Calibre worked on Bazzite. It does, and it's easy to do (once I knew it was there). So, that's where I am now.
EDIT:
But then along with the Bazzite (a new, containerized, immutable, atomic distribution) is new and therefore "bad" argument, we're back to flatpak (a new, universal application distribution methodology) is new and therefore "bad" argument.