If Atom is running and I choose Apple...Restart, the restart is always canceled.

To reproduce:

1. Launch Atom; an empty Atom with no open buffers is fine.
2. Choose Restart from the Apple menu.

Atom quits immediately, but the system restart aborts and displays the above dialog.

Also, this acts like choosing Quit from the Atom menu, which means that if you have unsaved but modified buffers, you lose them without a confirmation (cc #492).