Armor vs. Protection - question of piercing and negation

[PvK]

Protection is a combination of inherent protection (from toughness, thick skin, or whatever), and of external armor (from armor, helmet, and shield).

There are attack types that are armor-piercing(reducing armor effect by half).

There are other attack types that are armor-negating (no effect of armor).

My question is:
Do either or both of those attack types also reduce inherent protection?

PvK

(I think armor-negating, at least, probably ignores all protection, since it usually means a non-physical attack, like poison gas.)