A unit getting an ability is not damage applying differently randomly. Nothing in the rules set out in every other interaction of the game says a unit can’t have an ability. 99% of the game’s interactions say damage is applied uniformly.
OC is not “ok” because it’s a unique weapon. It’s “ok” because OC is what enables your ACU to leave your base beyond t1 stage. Having the game end based on who got to land the first OC and do 15k damage to an ACU is stupid gameplay. Same for ACU nuke doing 10k or whatever damage to another ACU. The exceptions exist because systems like OC or ACU nuke give positive utility that warrant the exception. Making an exception so Aeon gets some jank snipe unit when they already have the best t2 gunship for single entity targets is just not even in the false equivalency ballpark.