I have no idea why it looks like this out of the box, nor how to change it. It’s just the regular Atom install from Atom.io. I’ve installed on two PCs and a Mac and all of them have the standard black interface. Why would it install this way? How could we even get it back to normal?
This generally means that there is a fatal startup error that is preventing Atom from loading. Can you try navigating to the “Console” tab on the upper-right and see if there is an error displayed there?