Just another data point - I use nix + home-manager and have a bunch of servers set up like this;

  programs.ssh = {
    enable = true;
    forwardAgent = true;

    extraConfig = ''
      Host server-one
      HostName 123.0.0.1
      Port 22
      User root
      IdentityFile ~/.ssh/some_rsa

      Host server-two
      HostName 123.0.0.2
      Port 22
      User root
      IdentityFile ~/.ssh/other_rsa
    '';
  };