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.
This file is overwritten at every upgrade/installation. It is...
Requested by Crusade.
Simply unpacks a set of zip files into your StarMade folder, overriding existing files in the process if collisions occur.
Not more, not less.
Tool is self explanatory once launched, although you'll still have to find your StarMade installation folder yourself.