The issue is that /etc/nixos is in not that special, you can point nixos-rebuild to a completely different configuration file by setting nixos-configuration in NIX_PATH. And even if we modified nixos-rebuild to track the file, it would not be complete because most people probably split their configuration into multiple files. And even worse, the main body of options comes from other NixOS modules than the ones user created for their configuration so the diff would be full of noise anyway.
Not saying this is not something we are interested in but it would probably require a language support; and since it is a feature that can be easily achieved by version control (a thing most people already rightly do), I doubt anyone will implement it soon.