Apple ships some BSD and Linux tools (openssh, git) without changing how they store configuration, but anything written with macOS in mind has other methods. For example, Apple's command-line build tools for Xcode inherit GUI Xcode's settings and project files that are plists. launchctl uses XML plists in ~/Library instead of /etc. Daemons like Spotlight and Time Machine are configured via plist-editing GUIs or mdutil/tmutil commands.