Instead of having a single server.cfg file that is a mix of installation-time defaults and manual overrides, a practice I've seen really help with config management is to split the 2 purposes into distinct files.
server-defaults.cfg
This file is overwritten at every upgrade/installation. It is not designed to be modified locally and acts as the default value list and as a template/documentation file for server operators to base...
Split server.cfg into -defaults and -overrides
server-defaults.cfg
This file is overwritten at every upgrade/installation. It is not designed to be modified locally and acts as the default value list and as a template/documentation file for server operators to base...
Split server.cfg into -defaults and -overrides