What's the point of protecting your head when the entire rest of your body is stretched out, crushed under falling debris?
If I am going to be whacked by a whole lot of trauma, my priorities would rank protecting my head very highly. A broken femur can mend much better than a broken cranium. It soesn't take very much head trauma to turn your lights out permanently.
One reason you are urged to duck is that a lot of smaller objects in your surroundings will be flying missiles; again, a good reason to give priority to protecting your head.
If the building collapses, all of this won't matter a whole lot; you just by luck might find yourself surviving within a void.
Part of the scenario emphasizes that you are not likely to be able to move very far when the shaking commences; we will all have to do the best with what we have at hand.
The post about the high shelves in big box stores is very apt. They could be very bad places to be when the shaking begins.