NixOS in it’s current form does have it’s limitations but it’s ever improving. I personally have never had issues doing what I needed to firewall wise, but I’ve not done much of anything complex. Mostly just opening ports and a little port redirecting.

I’ve never used stow so I can’t speak to it specifically. Home manager is nice for two reasons. If you’re already using NixOS you can have one unified config for your whole system. And because Nix is a programming language generation these configs, you may be able to do thing you wouldn’t otherwise. It also has some nice defaults that you may not get without.

Because your Nix config also configures your software, not just installs it. Admittedly, with base NixOS that’s more true with server software than desktop. But with the addition of home manager you can also configure many desktop apps in your Nix config.

The #nix:nixos.org room on matrix is a great place to ask questions if you get stuck.