So either the current armor pen reduction needs nerfs or it needs some kinda of limitations.
Yes Lethality being unique would do a lot but that is not the only option.
Another option outside of nerfing all the stats could simply be making them not work together in a build.
Make black cleaver blocked out once someone buys LW or Lethality and vice versa like support items. It is intended to be a fighter item and this would not stop marksmen from being able to buy it if they really want to but would make them have to consider if it is better then buying LW against that Malphite or Rammus with 400 armor.
Then make only LW or Lethality take effect based on which one would ignore more armor. Similar to when someone buys Lich bane and Trinity force where only the one that would apply more damage has it's damage applied making it a waste to buy both together.
None of the items would need to be nerfed in any other way since there would be clear drawbacks to them.
Marksmen in general would be back to picking Last Whisper and Crit for contending with tanks mid to late game outside of a few exceptions.
Assassins would focus on Lethality and be trying to kill the squishes but far less useful against tanks with 300 armor.
Fighters would have the compromised middle ground item that is not as good as lethality against squishes and not as good as LW against tanks but what can you do when you are a Darius who has to fight both Malphite and Ashe one after the other. At least Darius can sleep well at night knowing he is making the enemies have less armor resulting in his allies physical damage being more effective.
Yes Armor can be ignored or removed to some degree but the amount to which it can be disregarded currently is too high.