yes, the p.def and s.def bonuses are applied after, meaning during the calculations for damage.
however, i would go for resilience. (many times i put my herja with +58 resilience on sancts instead because she almost never gets stunned. my ezK got only +11 resilience but almost 10k pdef added. all the defense and HP is useless if he keeps on getting stunned because regardless if he gets killed or stunned he wont be able to de-/buff either way.

