Cyclone has always ignored it too. Unchained's main usefulness is and has always been tied to the large amount of enmity generation that a WAR can achieve with the Defiance enmity bonus but having all enmity moves (not your stance specific moves) ignore the damage penalty. The only problem with Unchained right now is that it shares a cooldown with Inner Release which is tied to WAR's main burst phase and thus using Unchained sacrifices too much DPS to be utilized.
