DBUS system bus is independent of the applications and a sytem service started when the core sytem starts up. Applications have noting to do with the DBUS configuration and they are not overwriting it, just caring with their own sessions. If applications changing system setup on their own system stability is in risk and this is against any normal operation practice. DBUS offers a polite way to do it.
So my advice is to start DBUS system bus always if DBUS is installed. If no need to use it, just do not install the extension.