Abhishek,
A few days, I posted the reasons why MPC/PPC should not be used for level 3 isolation. Did you had a chance to read that?
MPC/PPC implement system wide isolation. IMHO, reprogramming it for level 3 isolation should be not considered as it creates various problems for the system designer.
You did also ask, how to ensure that security is actually enabled, basically if security has been initalized. The best approach would be to check if the SAU->CTRL is correctly set; if not the system should shut down.
Reinhard