At least from my experience, the only distro I have used that has offered any facilities in the package manager for handling config updates is Gentoo. Whenever there is a package update, if the default configuration files for the package change during an update, you are notified to run `etc-update`. This command then allows you to diff your current config with the new defaults, choose to use the entire file for the current config or the new default, or patch certain lines from the new default into your existing config.
Personally I find this super convenient, especially because whenever you perform a package update or install it will let you know whether you have any outstanding configuration files or important upgrade notes to address.
I'd be greatly interested to know if other package managers have these types of config and service management utilities. I looked around but I didn't really find anything.