Correct for data, not for config files. Config files are stateful unless you do the procedure I mentioned, because they're generated at first application launch.

If you try to symlink into an existing file Nix will indeed complain, which is why you have to erase the config file and then put yours in place. You can either write it out from a .nix file (pure reproducibility) or from symlink copy from a file managed by git (technically impure but effectively reproducible).

But my config files (/etc, ~/.config, etc.) are either managed by nix (and no program can modify them), or they are not and in that case nix will never touch them. In what situation would nix overwrite a file?