I use gnome, but it’s basically the worst DE, except all of the other ones that have been tried

It has the least features, so by default the least bugs.

I’m wondering why flatpaks don’t work for command-line tools

NixOS has NUR, but it’s not necessary because they take everyone’s pull requests in the official repo. I’ve been maintaining the software I use myself on the official nixpkgs, so I don’t need to use the NUR.