On much closer inspection it looks like the Safari buttons are all perfectly centered. But all the Finder buttons are about 2-3 pixels lower than they should be to perfectly centered. The arrows on System Preferences are 6 pixels from bottom and 5 from the top.
I guess the shading on the buttons make it look higher on Safari. It's possible the design team has noticed this problem and is trying different ways of trying to compensate for the visual effect the shading has on the eye.
I would have thought Apple would use the same buttons across all their applications. Well what's a couple of pixels here or there - especially considering its a beta!