Here's the thing... right now, Percent Armor Pen and Flat Armor Pen work together, becoming highly powerful. If we're tired of them being so powerful, another option is just nerfing their power, possibly to the point they're exclusively used together or against specialized squishy teams or tanky teams. Riot wants to leave a way for you to squeeze your Duskblade out early game and still turn around and Black Cleaver some use out of it when the tanks start bullying you around.
However, what happens when you flip it, and make damage penetrations mutually exclusive, or not work together? This makes both singular types less viable as well, which means their values should be going up to compensate. This, in effect, will cause specialized teams to be that much easier to counter with a single damage type, but also be just as oppressive against members of that type you want to hold back, usually the squishies.
Imagine what would happen if , for example, a Wukong had this buffed value and doubled up on the boosted Armor values? His 30% APen debuff would likely be raised to 40% due to not being as viable with Lethality, and then he grabs a Black Cleaver, which has now been boosted to 30% maximum. Suddenly Wukong is shredding 58% of all Armor on a choice tank target on Q-ulti instead of his current 46.8%. Or a Rengar getting 15 on ulti along with 18 on Duskblade and 7 on Lethality Rune when you'd currently expect 12, 16, and 5 at that point of the game. Suddenly you have a 40 APen early game up from the old 33, and that 7 armor is heavy on squishies that are already low.
Overall point, the fact that % and Flat Pen work together makes the values theoretically lower than they'd be if the two stats worked against each other. Because of this, you can build both together effectively, but cheesing strats on stacking only % Pen or only Flat Pen are less powerful, and in effect should only be truly effective on assassins who target backlines, juggernauts who target frontlines, or in games the enemy team overbuilds either tank or squishy.