Forgive the rudimentary nature of this question. I've always taken it for granted that I understood the rules for Penetration as they apply to Cover, but having recently reviewed the core, I feel like there is the possibility of interpreting these rules in two different ways. As usual I used the forum search engine in an attempt to find posts already dealing with this topic, and came up empty.
"If the shot would hit a body location that is concealed behind cover, work out the Damage against the Armour Points of the cover instead, with any excess being applied to the target as normal" - Rogue Trader, pg 246
It is the 'as normal' part that provides for the possibility of ambiguity. This results in two possible interpretations for how Penetration interacts with Cover:
1: The Penetration is reduced by the value of the cover prior to any damage being applied to the target's Armour. Example: A Rogue Trader fires a Plasma Pistol with Penetration 6 at a target wearing 5 Armour and taking cover behind thin metal with a cover value of 4. The Plasma blast tears straight through the Cover, leaving 2 points of Penetration that reduce the target's final armour value to 3.
2: Cover and Armour are handled completely separately. In the above example, the Plasma cuts first through the Cover, then effects the Armour 'as normal', completely cutting through it as well.