% Penetration

Someone please explain to me why having only a and no other magic damage built does tons of damage to enemies that have little to no magic armor? Yes it is % penetration, but there is no other magic damage built to then deal damage through that penetration. Also, 40% of a small amount of magic armor hardly takes away any of that magic armor because there's so little of it.

Secondly, why isn't there anyway to counteract % based penetration? Yes it is primarily built to counteract tanks who have a lot of magic armor/armor built, but you have champs like who just builds and ends up doing dumb amounts of damage to other assassins/mages who don't usually build armor. Or he'll usually start with because again most assassins/mages don't armor, and then when they start building he just has to build and the same as above mentioned follows.

Granted I don't play this game in a competitive/ranked scene, but I'd like to hear other people's insight or opinions on why % based penetration works the way it does and/or why there doesn't need to be any counteractions for a counteraction.