A lot of ircds disgustingly put some config options in at compile time, including things like the servername. A friend of mine had her irc server give the generic name for her ircd for several months because she couldn't be arsed to spend the time to recompile and reconfigure.
Couldn't you just make sure that puppet/chef/whatever runs the right config options? Maybe a script that asks you for values up front and plugs them in?