The only things that are effected by mods are the stats that you can get on mods. Armor penetration cannot be found on a mod, therefore mods do not effect it. As stated, it can only be increased through gear (if it is a stat on a gear piece that a character uses like the bayonet), through abilities (like Boba's payout), or through some character's relics (GAS' and JKA's relics give them accuracy, damage, and defense penetration).
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It is the best offensive stat in the game, but can only be found on a few gear pieces.
Possible to elaborate how you came to this conclusion?
I put accuracy arrows on all of my toons to beat that foresight
Make sure you upgrade them to 6E to contend with their evasion mods