Please implement /etc/PackageKit/conf.d.
Similar to /etc/apt/conf.d or /etc/yum.conf.d.
This would help derivative linux distributions (such as Qubes, Whonix...) to drop configuration file snippnetts rather than patching /etc/PackageKit/PackageKit.conf which is fragile with dynamic settings.
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.