The Penetration (Pen) of weapons with the Primitive quality only applies versus armour that also has the Primitive quality.
-Inquisitor's Handbook Appendix, Collected Weapon Tables pages 252 and 255 underneath the Primitive Weapons' Tables
This is in direct contradiction of an example provided by the Errata:
The Primitive quality on page 129
should include the addition:
“Non-primitive armour gets its APs doubled before being reduced
for penetration. For example, Guard Flak Armour (AP 4) hit with a
Great Weapon (Primitive quality and Pen 2) would provide 6 points
of armour: (4x2)-2.
So what gives? Do we, or do we not apply the penetration of Primitive weaponry? Personally, I would opt for the Example, otherwise primitive weaponry would be penalized twice for being primitive (once by doubling non-primitive APs against them, once for negating their Penetration entirely) and provide ample opportunity for Carapace-clad adventurers to go on a happy, care-free romp through primitive worlds with literally no risk of damage unless drastic action is taken on the part of the GM. Granted, adding the Penetration of primitive weaponry won't help a great deal, but it would certainly increase the viability of a player with a feral-worlder trying to create a compelling barbarian-type character.