I've used Ubuntu for a considerable amount of time and done numerous system updates. Please tell us what diffs you needed to perform, otherwise I call FUD.
From the blog you linked: "Dpkg keeps a checksum of the last installed version of configuration file. When it must install a new version, it calculates the checksum of the currently installed file and if it doesn’t match anymore, it knows that the user has edited the file. In that case, instead of overwriting the configuration file, it asks the user what to do."
If you didn't modify the system config you don't get prompted about what to do.
