I believe that I have proved it logically above in this thread that the final conulted institution is the supreme court and my other arguments also supports my opinion and hence the apex court becomes the most highly supreme institute. Other than that it depends on the circumstances and situations that who will prove himself suprerior either the apex court or the parliment!
Responding to your last line that whether the apex court can annul any of the clause of the constituton, my observations, as an administration is a case-study approach which is as it again depends on the case-study that does the clause made nul n void by the apex court truely reflects the islamic laws, emotions of the civil society and the people of pakistan? Then the answer will be NO, the courts can not do that! In this scenario a presidential reference can be filled against the CJ and if on the other hand, the CJ annul the clause that was against islamic rules and does not reflects the sentiments of the civil society and the people of pakistan than its possible for the apex court to shun the clause/section/order.
These days we are experiencing the best example of tug of war between these two institutions (NRO, NRO implementation case, 18th amendement case, judges restoration executive order - somo notice etc) for survival of their rival and soon you will realize that who WINS! and you will get a practical proof regarding the supremecy with respect to my arguments.