In general LSB guidelines suggest that /etc is for configuration files and /var/lib is better suited for "user state" or "application state" kind of things. It's generally best when packaging to follow that closely to avoid confusion, and it also makes it easier when working with lots of various programs if they are as consistent as possible.
In my understanding, while /etc is for config files per se, I took it to understand that it is for configuration files that the local system is using only. So, really anything that is not used to configure cobbler itself should probably not be in /etc. Any template file that is used by cobbler to generate kickstarts/configs that are pushed out I would consider application data, and thus should be in /var.
That's just my $0.02 though.
James C.