Random idea regarding Void/Whisper
Not going to pretend this idea is balanced, but it was a thought that just came to me.
What if instead of granting %Penetration Voidstaff/Whisper instead did bonus True Damage to the target equal to (percentage) of the target's magic resist/armor after accounting for how much flat penetration the champion has?
That would make flat pen and %pen mutually exclusive. In fact, they would be working against each other. I'm not sure how this would be balanced around DoT effects, though. But I'm pretty sure Riot could figure out how to make an ability only trigger once on DoTs.
EDIT: I just wanted to add this since a pretty large portion of the player base has only a tentative grasp of how the game's basic mechanics work. Right now %Pen scales off both the users damage AND the target's resist. This proposed change would make it scale ONLY off the target's resist. This is part of the reason why %Pen is one of the strongest damage amp tools in the game, because you're double-dipping the scaling.

. Then youll have no resistance against the Magical and physical damage and if you do, this thing your proposing does TRUE damage, which is why they removed the
true damage on every auto. It was OP and turned
into weedwick nuker. Tanks already have it bad enough, penetration is insane, % hp damage is insane and resistances are shit.