[Phoenix-D]

When Penetration damage is being applied, Shields are treated as one unit. Armor is NOT.

What does that mean? Say you have a damage type that has 50% penetration of both shields and armor. If your ship has two shield generators and one armor unit (300 HP total), the damage goes like this:

100 damage hit. 50 absorbed by shields, 50 passed to armor. 25 absorbed by armor, 25 passed to internals.

But if you have one shield generator and two armors (300 HP total), it goes like this:
100 damage hit. 50 absorbed by shields, 50 passed to armor 1. 25 absorbed by Armor 1, 25 passed to Armor 2. 12 absorbed by Armor 2, 12 passed to internals.

It only gets worse as you stack on more armor. This applies even if the shield generators are of different types (one Phased and one Normal, for example).

Speaking of shield generators, mixing two different types is a Bad Idea. The shield points are combined into one pool and the LOWEST numbered shield in ShieldAndArmorTypes.txt is used. Armor doesn't have this problem since the armor types aren't pooled- a weapon that skips normal armor WON'T skip Emissive armor if its mixed with regular.

The Emissive ability is also applied to each layer of armor, at the first step. Take that 100 damage hit again:

50 gets through to the armor. Emissive knocks off 10 points right away. 20 damage is applied to the armor and 20 goes to Armor 2. Its emissive ability knocks off another 10 points, so 5 damage is applied to the armor and 5 to the interior. So if the ship had just three Armor components, no damage would get through at all!