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If you run the Emacs flatpak program, there are restrictions. By default, there is limited access to the session D-Bus, and no access to the system D-Bus. You must enable access to services living outside the sandbox like
# flatpak override --talk-name=org.freedesktop.secrets org.gnu.emacs
‘org.gnu.emacs’ is the Emacs flatpak application, and ‘org.freedesktop.secrets’ is a service you want to talk to, for example.
Access to the entire bus with ‘--socket=system-bus’ or ‘--socket=session-bus’ stops the filtering and using them is a security risk. So they must be avoided.
Service names might be mapped when arriving Emacs. For example, you will see the ‘org.freedesktop.DBus.NameOwnerChanged’ signal for service ‘org.freedesktop.portal.Flatpak’, even if you have registered the signal for another namespace.