WHy cant pen only apply to defenses bought?

Because it would be pointless for assassin's to buy armor penetration in any way.

The same reason the only armour pen item crit ADCs need only applies bonus damage

screw crit adcs

well there is items that do this such as that ignores 45% of bonus armor

that is any armor you naturally dont scale ... so runes, masteries and items are reduced by it but not your natural armor

Then flat armor penetration which is designed to be effective against squishies would now become useless vs squishies and pointless vs tanks. The stat would have no reason to exist.