Is not an easy task for packages that provide integration between other packages in the archive to be policy compliant. According to the Ubuntu policy a package cannot modify other package's configuration files. Some techniques has been introduced to help on this task, from dotdee [0] to augeas [1], discuss with other developers how to deal with this situation that also affects other configuration management software like puppet, juju, etc.
[0] http://blog.dustinkirkland.com/2011_04_01_archive.html [1] http://augeas.net/