That's mentioned briefly in the optical compensation bit - visual center is what looks like the center, mathematical center is just the middle of the bounding box. Triangles are the obvious example, but even more annoying is logos where you have the ® or ™ at the end, which have very little weight but are included in centering math on badly cropped logos.

That's called optical alignment. He somewhat mentions that with the Apple logo example.

I think it's true of some of the other Apple examples that he's put lines over, they look optically correct.