[OceanBlue]

Shirou is still limited by his physical ability. Even if he has the technique to block it, he doesn't have the speed nor the strength required to block Berserker for a prolonged amount of time.

Originally Posted by Type-Moon Wikia

Emiya Shirou can evaluate the idea behind the creation, determine the foundation, reproduce the base material, copy the manufacture, assimilate the experience, reproduce the age; unlike a normal person who does the recreation from the base idea, he will include in the blueprint the material property, the nature and the history of the item.

Emiya manages to slash off Berserker's arm in the game, and does a pretty good job defending himself.

The golden sword does not stop and, as if being pulled toward it, slashes through the giant's arm.

I hear a gasp.
In front of me is the axe-sword swung like a storm and a defending sword that is being made.

I don't know if I'm desperate, but I'm blocking the attack with the sword in my hand.

I made the sword that surpasses Berserker.
But that's all.
As I am only a maker, I cannot handle the sword--!

Unless we're talking about the anime, not just projection in the T-M universe in general. If we're talking about the anime only, then you're just going to have to accept that it might not make sense.

By the way, I choose All of the above.

Edit: I don't understand the other question Blade, so I can't clarify [And Dragon edited out the example, so I have no idea what's going on.].
Archer's Noble Phantasm doesn't control Archer's body. It's like learning how to paint. You can still paint in the way before you learned how to paint, but you can also use your newfound techniques in painting. But in fights, it becomes a lot more instinctive, and I'm guessing sometimes you automatically use your techniques to defend yourself.