Absolutely! I'll give you an example. In the NixOS config for my desktop I have the lines:

{
  environment.systemPackages = with pkgs; [
    firefox
    ...
  ];
}

So Firefox is installed every time I build a system with this config. This is just like apt-get install firefox in that very user can use it after installation. The config lives in the respective user's dotfiles (.config/mozilla/firefox) and will of course survive reboots.

What I chose to do additionally (but this is in no way required!) is a home-manager config for my main account with the lines:

{
  programs.firefox = {
    enable = true;
    policies = {
      DisableFirefoxAccounts = true;
      DisablePocket = true;
      DisableTelemetry = true;
      DownloadDirectory = "${config.home.homeDirectory}/tmp";
      OfferToSaveLogins = false;
      ...
  }
  ...
}

This is a declarative configuration that basically handles my dotfiles (profiles, extensions, themes, ...) for me. I think you have the impression that this is mandatory, but it is really a very specific behavior through the home-manager module, but you can absolutely run NixOS without it.