I think the author generally made some good points there, but something important was overlooked in one of his examples.

  git checkout master

You might notice there, the front command, 'git'. This wasn't launched from a special git command line, it was launched from the same command line that he was using for everything else. On the GUI side, on the other hand, you either have to to Alt-Tab some undefined number of time -it might be 1 or 5, you have to do it slowly and pay attention to visual feedback. For the CLI, on the other hand, you just type three letters and the correct context appears.