I am currently configuring FCCU NCF Fault Reaction on MPC5744P as SBC Reset / Functional Reset (all of them).
But I wonder if I should try to clear the faults some times (like 3 times) by interrupt before triggering a RESET?
What do you think in case of System stability vs Functional Safety?
Well, this is defined by the safety standard which your application is targeted for. For example ISO26262.
Usually the faults are not cleared before reset, but after reset as the faults are used for analyzes.