The 'commission' was most likely a court-martial was it not? I do believe that has already been explained in some detail.
Do you understand how the French legal system operated? The military courts-martial/tribunals were specially convened to try special cases and in Dupont's case, an Extraordinary Council of War (court-martial) was established in 1812. Those councils of war were established to try general officers in cases such as Dupont. That isn't 'outside' the legal system, but part of the military justice system which Napoleon had every right to establish. And they were outside of the civilian justice system.