> without warning, replace your config files and update software to versions incompatible with the previous.

This is just nonsense, pacman doesn't do this. If you'd modified a config file, it will create a .pacnew version instead of replacing it. Otherwise you'll get the default config synced with the version of the software you've installed, which is desirable.

It's pretty rare to modify any config files outside of ~/.config these days anyway. What few modifications I have at the system level are for things like mkinitcpio, locale, etc and they never change.