Why would I have to manually set it when the memory is 1600MHz 9-9-9-24 at stock?
Because the CPU doesn't offically support that memory speed. So it will boot up with your memory sticks at a lower speed like 1333MHz and then that is when you can go in and set the memory speed and timings to the proper specifications of the memory sticks.
This is a very common occurance for basically everyone who has bought memory at 1600MHz or more, i actually had to manually change the memory speed and timings for my 8GB Corsair Vengence kit (1600MHz) as well. This because my 1055T does not offically support speeds higher than 1333MHz.
This is changing though, for instance the Core i7 3770K offically supports 1600MHz memory out of the box. But again anything above that will need to be manually set.