I can’t speak for other distributions, but Pop!_OS has had a “Refresh Install” option for a while now that does exactly this. This hasn’t happened often, but there have been a couple of times when something borked my system to the point of making it no longer boot, and re-running the installer in “Refresh Install” mode got everything back and running within 30 minutes while preserving all of my non-system files; in particular this meant that I didn’t have to re-download my Steam and other locally installed games, which is significant because they are the largest apps on my system.