I just found a legendary Penetrating Combat Rifle and pondering its effectiveness. The description for 'Penetrating' is stated as: Ignores 30% of the target's damage and energy resistance.

Now my questions are, where does this 30% come from? and how does this effect Armor Piercing perks and weapon mods?

I am assuming it means the 30% reduction is taken from the armor. If that is so, how does that relate to the Rifleman perk? Which states that it ignores 'Armor' not Damage Resistance.

Also, would they all stack like so: Penetrating x Rifleman x Armor piercing mod?

I *think* they all stack, but I'm not sure what the exact math would turn out to be, especially since total damage is based on a ratio of damage to DR this time instead of a flat percentage reduction. Regardless of the wording, all three effects are the same thing: ignores a percentage of the target's armor rating, ballistic or otherwise.

You also won't be able to ever get all three, since armor-piercing is only on automatic receivers - adding one of those will put that weapon under the Commando perk instead of Rifleman.