a "harmless" OS upgrade can potentially break your serious mission-critical systems

This is true of anything running on the machine whether using system perl, user-built perl or not using perl at all. If this is the sort of thing which concerns you then you may as well go the whole hog and containerise your perl and applications.

I'm in the opposite school here and am perfectly happy to use the system perl, perhaps because I am also the sysadm and therefore my O/S upgrades are planned rather than being surprise events. This ensures that all my applications can be tested in development on the new O/S before the upgrade gets anywhere near to production. It's the approach I have been following for many years (the last user-built perl I used in production was 5.6.0) and has proven solid.