Added armor was not put in to combat armor pen as it was put in for the S2 gear at which point no one had armor pen. S3 has no added+added armor; S3 had the extra armor from S2 + the base amount which scales with iLevel.

As an aside, armor pen is a dumb idea in PVP. EA/SA/AP are just far too powerful against casters when Blizzard is balancing around them having *some* armor; if they weren't balancing around this fact then they would not have wasted iLvl points on the additional armor in S2 as casters loose 100% of their armor with 2 of these abilities.

And... some stamina was added back onto the sunwell T6. For example, Slayer's bracers/belt/boots now gives 64 stam (you'll get the socket bonus) versus 131 stam on the S3 items.