Personally, I wouldn't be leery of upgrading Net::DNS via CPAN at all. It's probably better than upgrading perl modules with yum or apt-get, since CPAN is pretty much the authority on perl in general.
As stated earlier, he is right to be leery, as updating via CPAN does *NOT* inform rpm of the changes. This means that anything which requires the perl-Net-DNS package will fail with dependency errors.
Also, while CPAN may be the authority on perl, they are not the authority on PACKAGED perl, as it ships with any managed distribution. Your methods show you to be working against the benefits of package management, and therefore, administrative sanity.
You can just as surely get apache from apache.org, but why duplicate the effort when the distribution has taken the time to test, patch, secure and configure the software for you. Unless there's a compelling and convincing reason (and I have yet to see one) you should ALWAYS use your distribution's package management scheme. This applies to all distributions, and manners of package management with the exception of slackware for obvious reasons.