Maybe I am vastly underestimating it, but I could imagine this being buildable atop of nix quite straightforward?

Yes because both flatpak and nix use bubblewrap and linux. So it is indeed possible to build it with bubblewrap.

GUI apps on NixOS rarely care about sandboxing so while you can do it yourself i bet almost noone does. Flatpak is trying to give you basic protections out of the box.