Code:
flatpak --command="bash" run com.calibre_ebook.calibre
And now you can do your command line Calibre stuff without problems. But yes, if you're trying to use flatpaks with anything outside of the packages? That's a pain and you have to muck around with Flatseal and permissions and it's just easier to use the native packages at that point.
Still a lot better than Snap packages. Those are the worst.