You are trying to remove critical packages, see here: Updater is removing local packages
If some configurations are override by updater, than it is fault of package it self (being confident that it isn’t udater bug). There are two options why it happens, it can be because file isn’t specified as configuration file or because there is some post-install script that does something to that configuration. In both cases it requires fix in package it self. What package is causing you problems?