Could someone calrify

Along with runes, it would be considered regular armour pen.

With AD, some things say bonus and others don't, which indicates whether it takes only the AD acquired from items, and not what you had before the game started. HOWEVER, I don't think a "bonus ap" thing exists in the game, and all ap scaling skills and items are just referred to as AP, meaning it's all bonus AP (because without items, runes, or masteries, you always start at 0). Except outside of runes and masteries, no champion innately has armour pen that isn't brought on by a skill or item. I don't even think there's a skill or item that scales with specificially "bonus armour penetration", so it shouldn't matter. Treat it like AP, I say. It's all bonus, except what you have before you enter the game.