No, nix-env installs to your user environment, which the nixos-rebuild command barely touches. It doesn't touch the global configuration file. In fact you can even manage user accounts imperatively.

My approach is the following: try a program using nix run (or nix-shell, depending on the case) and if it does what I want, add it to my configuration and nixos-rebuild test. It will then be available permanently on next update.

What I also do is keep all nix-related files in a git repository under main user control and have the flake.nix (if using flakes, otherwise configuration.nix) soft linked into /etc/nixos. This also enables rollback on your configuration, not only on the actual system state.

I agree that each package takes more time, but OTOH, you save a lot of time and effort in the longer run. Also I don't really have that high fluctuation of packages that it actually matters.

home-manager is a bit in a weird spot in my opinion as in it's not very clear how it should be installed. If it's a NixOS module, your changes will only be applied during rebuild - which only root can trigger. But if you're already triggering those as root, you might as well as the packages globally. I generally install globally and configure the options using home-manager.