So...my brief read of that link is that if you open Atom in a directory that is already a Git project, then Atom knows how to do some Git-related thing. That would seem to imply that you need to initially set it up manually (or via GitHub desktop tools) on your computer before Atom can do any Git-related magic.
That's how I always work: using
git clone <repo string from github> or
git init <repo_name> so that I have an applicable directory,
cd to that directory, then open VS Code in my case with...