It sounds like you're talking about home-manager, which is a third-party Nix module, not Nix itself. I've been using Nix happily for several years now for work and personal without needing to use home-manager at all (since I don't like it either).
If you use Nix you're completely blind to that unless you A) religiously check your state or B) use another tool like 'git' or 'nh'. Like I said, it's a blind spot, both figuratively and literally.
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).