Are you sure that s.th. called "secure boot configuration update" is delivered as a flatpak and not as a native package?In the latter case the update command would be e.g. apt upgrade on Debian based or dnf upgrade on Fedora based systems, or whatever the package manager of the distribution is called.
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Magic Mushroom
At least the Debian package depends on both, the library
libfwupd2andfwupd. Sofwupdmgrshould be present too (depending on how the used distribution handles these dependencies).