Magic Pen or Armor Pen? (For AP scaling)

So in cases like E (100% ap scale) or (Some ap scale) would these abilities benefit at all from magic pen if you built ap? Or would the magic pen just be worthless since their output is primarily translated to Attack Damage? If so would it make more sense to build armor pen on an ap build?

Sorry I know this is very specific, I am just confused about how it works. For example if you built all AP because of the scaling, the damage I presume it still translated to AD regardless, at which point would armor pen boost that damage output with an ap build? It's very confusing.