On a picture of the movement in the 5959 watch on page 43, notice the Geneva Seal isn't perfectly contrasted.
The engravings are done when the metal is still in the brass-yellow form. The engravings themselves are then covered with a protectant (usually a gel) and then dipped into a rhodium plating bath to cover the brass-yellow parts with the rhodium finish. The gel is then removed and because this part of the metal was not exposed to the rhodium plating (because it was covered with gel) it retains its original color.
It looks like this Geneva Seal had its gel applied very slightly more liberally than intended.
Still doesn't affect the beauty of the watch however, notice the completely polished column wheel and the otherwise perfect finishing of the movement. Magnificent!