Core Policy versus selinux ebuilds

Is there a difference between policies that appear to be in core but 
also have their own ebuilds? For example: selinux-ddclient versus 
policy/modules/contrib/dnsmasq.* and selinux-ddclient versus 
policy/modules/contrib/ddclient. I need to change both but when I tried 
to change dnsmasq it started complaining bitterly about binding to 
random ports, which is what dnsmasq does.

Just to be absolutely clear, I expect that there is a versioning 
difference because I have pulled the latest from the git repository but 
I am using stable ebuilds, but I don't expect that this is the difference?

Thanks in advance,

Robert Sharp