I use pkgsrc extensively on CentOS and my take on avoiding duplication
is "don't install the Yum version if it's avoidable". I keep my Yum
installations to a minimum and use the more recent packages from pkgsrc
wherever possible.
I also want my pkgsrc installations to be completely self-reliant to
avoid unpleasant surprises, so I always set
PREFER_NATIVE= no
PREFER_PKGSRC= yes
in my mk.conf.
To avoid leakage issues, I actually build a full set of binary packages
in a minimal chroot, and only build from source on a production system
if I need an optimized or customized build.