There is probably some trickery going on to optimize e.g. completely hidden elements. But when you compare the two options of "loop through the rectangles from below and for each pixel in the rectangle set its color" and "for each pixel, determine the rectangle it is in and set its color accordingly" the amount of work is not much different. You could speed up the second strategy for nested rectangles by using a smart search structure, but this will most likely be trumped by specialized rendering hardware that can paint lots of rectangles very fast but isn't very good at branching logic.
