Sorry, I'm not really helping here, just to say I get the same behavior at work. For information, my game is quite heavy on Web GL effects.
At work (on a Sony Vaio laptop, a bit old but decent): Chrome Fullscreen is 10 FPS more than Node Webkit.
At home (on a fat powerfull MSI laptop), I get the opposite, the Node Webkit is 60 fps rock solid, chrome fullscreen is 50fps.
So, I don't know how to explain it, but yeah, I see what you mean.