For any consolation, I have a Mac 10.12.3, now with Atom 1.17.2, and the icon is saved on my Dock.
I thought I used to have this problem with earlier versions of Atom, even to 1.12 or before.
I remember clicking to re-open Atom, in case that was incorrect.
Updating even today to 1.17, it was working, even waiting with the editor closed for more than 15-20 seconds.
I reopened Atom, clicked update, and proceeded to wait again, and after a similar while, it opened by itself, and was updated.