But the major advantage of this is, because user and system data are now strictly separated, it is possible to completely delete and replace macOS without affecting user data and configurations. The main reason was safety/security and reliability: Third parties are no longer allowed to modify the core system. In recent versions of macOS (I think starting with macOS 11?), Apple started strictly segregating system data from user data. You should not lose all your configurations in the event of a reinstall/restore today. But I don’t think the problem you stated actually exists. I also spent many years maintaining bootable backup clones of Macs.
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