The (experimental) 3.0 commands use the flake registry, not channels.
This comes with a hard-coded list of default entries, one of which is nixpkgs - this one currently points to the unstable branch of the GitHub repo.
Up until recently there was no real alternative (for flakes), but a recent change introduced “lockable tarballs”, which makes it feasible to lock to the channel tarballs instead of a raw git repo. This has a bunch of benefits, but the default registry doesn’t currently do so.
All that said, you can change your registry imperatively so that it uses those tarballs, e.g.:
$ nix registry add nixpkgs https://channels.nixos.org/nixos-unstable/nixexprs.tar.xz
It won’t solve the rate limit for anything not rehosted by hydra, of course, but anything that’s prebuilt in the cache (or projects whose sources are hosted elsewhere) should no longer hit GitHub.
If you use NixOS or home-manager with flakes (which I urgently recommend over using nix profile, let alone nix-env, by the way, precisely because the other commands implicitly depend on this imperatively maintained flake/channel list that you don’t know about), changing your flake’s nixpkgs input to that URL should also fix ratelimiting, since both projects include some code to change the registry’s nixpkgs entry to their nixpkgs input.
The default should probably be changed, tbh.
You can also of course use the 2.0 command equivalents and sidestep the flake mess, but I recommend using nix-shell and never nix-env.