Don't know how you installed it, but required permissions are usually shown and warned about. The CLI could be clearer, though, but shows that host filesystem access is granted to calibre when it prompts to install
During installation they're _mentioned_ but the you can't pick which permissions to grant. If the developer requested it, its granted by default.
There are third party tools to tinker with permissions, but even those tools follow a "implicit grant first, revoke later" model, mostly because of how Flatpak implicitly grants permissions.