The truth is almost exactly the opposite of this.
There was a bug in the combat code for some time that caused raw CS to be used to determine damage, rather than having it determined by Weapon quality with other modifiers (that don't include Armour).
I have since fixed this bug, so for at least the past 2-3 years, Weapons and Armour have, indeed, been clearly separate. (There may still be one or two minor places in the combat code that don't separate them as much as they could, but nothing like the degree to which the other bug affected it.)
The new RC construction system changes absolutely nothing about how weapons and armour are handled in combat.
Whoever told you this, I strongly encourage you to tell them they're full of crap.
