Excellent points and thank you for bringing them up!
(1) "Target Area" is already defined in 3.1. You would have to add a definition in there for armor.
I would argue that the proposed 3.6.1 is defining a new subgroup of optional target areas, but I can certainly see where the argument could be made. Perhaps add in something like "3.1.7. Armor is considered separate target areas from a combatant's target areas."
(2) Your new proposed rules cause a lack of clarity around ranged attacks to heads, due to the existing rules. While the end result can be figured out by reading over the rules, I feel that this makes the rules less clear rather than more clear when it comes to head shots.
I really just don't see where the confusion is. Perhaps a slight reword to, "A Class 4 Weapon striking an head armor target area causes no Injury," but otherwise it seems pretty clear to me. Arrow to helmet = no hit. Ditto for Class 5. Could you explain in more detail what you found confusing?
(3) Since head armor is now a new target area (Not part of the head) you would have to clarify that melee weapons can't strike this target area.
Excellent point. Perhaps, "126.96.36.199. The Head Armor Target Area is likewise an illegal Target Area for Class 1, 2, and 3 Weapons and a legal Target Area for Class 4 and 5 Weapons."
(4) Armored areas don't take one handed stab damage. Two-handed stab damage goes through the armored area, but keeps the armor intact (By most interpretations). Not sure how you want to address this.
At this point it is important to note that I did write these assuming the Rules Revision would pass. Perhaps a little optimistic, but I had to pick one so I went with the one I thought was better. So, using the Rules Revision wording for stabs,
3.5.3. Class 3 (thrusting) weapons wielded one-handed cause one hit of damage to an unarmored target area, and have no affect against an armored area.
188.8.131.52. When used two handed, Class 3 weapons bypass armor.
This neatly ties everything together. No damage to armor on one handed stabs, and the armor is completely bypassed (dealing damage directly to the underlying target area) on a two-handed stab. And since the armor is bypassed it still functions as a separate target area. This point was really one of the main issues driving me to do this rewrite of the armor rules, as under the current rules this is no way to write a rule that does this without a full armor rules rewrite.
As mentioned, I did intend to pair this with the Rules Committee Rules Revision, because honestly the current BoW is a mess and adding another patch onto it at this point (especially one of this size) would just be ridiculous. But I wanted to get the conversation started early so that hopefully all the issues can get ironed out before the next voting period. So thanks for the comments!