Because shotguns were implemented and people kept asking how armour and such worked. Also because night battles have been a thing.

The final formula is surprisingly easy:

(Final Attack Power*(rand(0.85 to 1.15)) - Effective Armour.

...Myep. That's it. 1 to 1. Minimum of 1 damage. Criticals are calculated after the armour layer of the damage formula.

Armor Penetration reduces the  effective armour of the target by 1, to a minimum of 0, so having more AP than the enemy has armor doesn't really do much (it does result in 2 extra damage if you overmatch, but it doesnt matter if it exceeds by 1 or by 100). All G&K t-dolls (that is, ours) have a base AP of 15, so low enemy armor is meaningless. SF have a base armor pen of 0, and very few of them have it (the ones that do though tend to have so much armour pen that using shotguns against them is largely pointless.)

What this does mean though is that since armour is 1 to 1, sufficiently high firepower can bust right through armour even without AP rounds. This is largely how night rifles like OTs-14 and such can defeat armour - Just doing so much damage that it doesn't matter. As a warning though, some later enemies have immense amounts of armour, such that this method becomes much less practical.

Also, besides AP rounds, many skills also outright ignore armour. Grenades, Molotovs, etc. and the like all ignore both armour and evade, making units like Vector handy to have around at times.