i think they are saying that each benchmark is geared to fully and throughly benchmark a diffrent part of the computer
3dm06 will bench your vga card to its fullest
and super pi is a really good benchmark for cpu's
im guessing you like the idea of one number for the whole thing. but thats a general BM but for all you know one part of your pc could be bottle necking or bumping your score. where these two benches show exactly what is going on with your hardware. your cpu could be oced to the max and bumping up your score wile your vga is not quite up to scratch. or vise versa. with the two you know exactly what eather is doing.