Or if not, is there a way to make yum be aware of them? Does 'rpm -qa' and 'yum list installed' query the same source?
2 Answers
Yum is aware of packages that are installed or updated via the rpm command. As proof for example you could manually install an outdated version of a package that is available in an upstream repository via rpm -ivh <package>
and then run yum clean all && yum update
and it'll update.
Both command uses rpm db files under /var/lib/rpm/, yum is a only a python script to manipulate the rpms