They don't, it's an illusion because the background is a flat grey and some icons are darker than others.
It's consistent because every icon has a gradient, even if subtle - in contrast with the original, where some are flat and others have a 3D effect from the gradient, and some even have a gradient on the opposite direction making a complete mess of convex/concave illusion on the home screen.
It's also consistent because all icons have just the right amount of detail. Compare the safari, clock, compass, notes, reminders, newsstand and passbook icons.
Lastly, he modified the margins back to the original proportions, which are better balanced. Compare the iTunes and App Store icons.
