This is true, but in my experience it has mostly been pretty easy to deal with. Generally it's just a matter of re-linking /etc/zprofile and friends to the ones

This is true, but in my experience it has mostly been pretty easy to deal with. Generally it's just a matter of re-linking /etc/zprofile and friends to the ones from the nix-darwin installer (if you're using nix-darwin, which I would recommend).