Mostly they are unbroken. At least the most of the time. They do perform their functions the best way they can.
And this is my point. They can't "decide" the output. The input "decides" the output.
So far as I can tell you're agreeing with me, or at least arguing at a right angle to what this post was intended to discuss. Whether it's the brain or the input that does the deciding, there are some combinations of brain and input that produce results that may be contrary to one's conscious preferences.
The fact that all brains work in roughly the same way doesn't change the fact that they are not the ideal substrate for rational cognition in a modern environment.
A few examples (in approximately increasing order of controversy):
If you proceed anyway...