This is something I just had a thought about that I was wondering if anyone here knew about? I know that the NCR actively seems to hunt down anyone who seemed to have any kind of of association with the Enclave. Even people like Arcade in New Vegas who was only an infant when Navarro went up in flames could get arrested for war crimes he had never even been apart off. So if the NCR goes hard against Enclave remnants why aren't they same with remnants of the Master's Army like Marcus? If the Master had gotten his way, the NCR as we know it wouldn't have existed since the mutant army would have either ransacked the towns that would later make up the NCR for people to toss into a vat of FEV or destroyed them for resisting. The closet thing you get is general super mutant persecution from people just being afraid of them, but nothing on level of putting them on trial for war crimes.