Since this is a video game, its events depend on the mood of the writers. If Fallout 2 was adapted into a real-world scenario, they would have simply pressed the button and cleaned every place and hole of the globe without anyone knowing.
Since the whole idea of the world existing exactly like it does in the Fallout series is ludicrous, then the Enclave wouldn't exist if this was real life. You can't bring the Enclave into real life, as they are just part of the imaginations of Black Isle Studios, and now, Bethesda. They didn't win in the game, so they couldn't win in real life if they existed. The Chosen One would still have destroyed them. You mean they would have won if The Chosen One didn't exist in the same world as the Enclave, but he/she did, and he/she did destroy the Enclave. Now, the Lone Wanderer destroyed the Enclave. They lost and haven't achieved anything other than the state the world is in in the Fallout universe and the killing of their fellow humans. They have lost, and there is no chance that they would have won because they were meant to be the evil antagonists who would lose from the very beginning. To try to change lore is ridiculous and to insist that they would win in real life is ridiculous as well. They couldn't even exist in real life, and if they did like they do in Fallout, the Chosen One and the Lone Wanderer would still have finished them off. The only thing that didn't make sense was the Enclave coming back from the dead in the first place. The Enclave lost and achieved nothing beneficial. Mods and the imaginations of Enclave supporters will never change that.