if the files are (config) type, then a locally user modified version will superseed the new rpm based one, and will result in your config's being left alone with the new files being dropped as .rpmnew I'd presume this is what happened ?
Not in this instance no. 90% of users have no reason to modify /etc/issue, /etc/redhat-release, or /etc/sysconfig/rhn/sources, so these files will be overwritten most of the time. While adjusting our packages so that they can be used on both RHEL and centos isn't exactly a centos specific concern, it is the neighborly thing to do.