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I'm fairly interested in history, too, as it happens. I am aware that armour didn't have unnecessary holes in it for enemies to poke their weapons into. I am aware that people wore armour despite the weight and expense because it worked. I am aware that even early firearms had trouble against good steel, to the point of being used to leave proofing marks.
...To execute an unconscious soldier, the foe should remove armour pieces and slay him that way, or bash him with sufficient force that he is killed despite the armour...
You're right. Historical soldiers did prefer to go around armour, or remove it if they had the opportunity, rather than bash away uselessly like mindless machines.
The problem here is that we're talking about DF, in which our soldiers
are mindless machines. Nobody will pull a misericorde, nobody will go for an eye slit, nobody will crush anyone's throat... nobody will do anything but flail randomly at each other until one drops, at which point the other will hit them in the head until they die.
If you go into Arena Mode and pit two steel-armoured swordsmen against each other, they will futilely biff at each other until one passes out from exhaustion, at which point the other will relentlessly chop at the helmet until he too collapses. One will come to, scrape at the other's helm, pass out, repeat. This can continue almost indefinitely.
In Vanilla, an elite soldier with an iron weapon can almost literally never beat an unskilled conscript in full steel armour.
Try it - in the arena, plonk down two guys. Give both iron short swords. Give one full steel armour. Give the other a buckler and master-level sword/shield/wrestling skills. Watch as the former beats the latter. Repeat as many times as you like. Get the same result almost without fail.
I think we can agree that this is ahistorical.
Now, if 2% of hits ignore armour, then a warrior that can casually land a hundred blows to the enemy's one will reliably win, despite inferior equipment. And a heavily-armoured veteran will be vulnerable to getting swamped and killed by overwhelming numbers. Neither of these are really represented in Vanilla.
The miniscule failure rate is not meant to represent a gaping hole in the armour. It's a compromise, meant to cover the deficiencies of the DF combat system, in which soldiers will blindly attempt to hack through the masterwork adamantine helm of a downed opponent rather than open an unprotected femoral artery.
I assumed that since you're clearly already open to modding, you might appreciate a suggestion on making the results of combat more closely reflect reality.
And it was just that: a suggestion. If it violates your principles, nobody will force you to use it. Was trying to be helpful - sorry.
P.S.: Mail shirts are by default marked as COMMON in the entity file. This means that virtually all Dwarven civs will be able to make them... but not all. You probably just got unlucky and picked the rare Dwarven civ that never invented the hauberk. FORCED will ensure that every instance of that civ in every universe will be able to make that item.