The blockBehaviorConfig would be overwritten, because it contains the values that would change if a Dev was to rebalance Shields or thrusters.
Plus, the game just downloads the Builds, and extracts them while overwriting Existing files o -o and that file is included in each build.
Server.cfg doesn't seem to be included in the fresh build files, But is instead auto-Generated when you first start Starmade (in the case of an update, and new options being added, they are added to the config).