This article picks on Atom, but it's really arguing Vim vs Every Other Text Editor based on composed commands vs monolithic commands.
I agree that Vim's style of composed commands is somehow more natural. But Atom's core value is hackability. Atom's vim-mode package performs every operation in the article and countless more, and does it all without any special APIs or permissions. The commands that are not in the editor API, or are but are slightly different from Vim, are written using editor primitives. That hackability is Atom's special sauce, not the set of convenience commands the editor API supports.
Sublime would have been a better "target" for this comparison.