You can use NixOS on the desktop -- it has a lot of benefit (including atomic upgrades/rollbacks). But it only really works well if you manage everything through Nix. Other mechanisms such as the ones that you mention tend to break very often.
I just gave up using Flatpaks with NixOS and install GNOME extensions through Nix.
I tried to setup a simple NixOS machine this week. From this experience I couldn't manage to install any GNOME extensions via the browser plugin because of some Firefox manifest location that conflicts with the way the NixOS store handles it - there is some workaround in some tickets, but it made me wonder how many other applications are in need for specific workarounds. I then enabled flatpak via the OS configuration, but the first installed app couldn't launch because of some obscure error with gstreamer. I changed to fedora and could setup anything without any of those issues.
I really want to like NixOS (I still do), but I now consider it more for a server environment than a casual desktop environment.