There is a new emerging FHS that recommends storing writable state/configuration data into /var/lib/<id> instead of /etc/<id>. It would be nice for PackageKit to do that as well and to leave /etc empty by default.
Or even better, just read system defaults from /usr/lib/PackageKit/* or compile them in and not need a configuration file at all by default.
We moved the upstream bugtracker to GitHub a long time ago. If this issue still affects you please re-create the issue here: https://github.com/hughsie/PackageKit/issues
Sorry for the impersonal message, and fingers crossed your issue no longer happens. Thanks.