Skinweave:
    Skinweave is artificially reinforced skin.  By the logic R. Talsorian uses, there would be a penalty for unaltered skin.  (most will say "there is a -0", zero, being neither negative, norpositive doesn't constitute as a penalty)  Skinweave, at higher levels, gains its own penalties (both in ATTR loss and REF as I recall), therefore additional layering penalties fail to apply again.

    Subdermal Armor:
    Well let's consider this one as well.  Subdermal armor is replacing bone with obvious protection (a network of linked metal plates buried underneath the skin).  This causes loss of both reflex and attractiveness.  Once again layering penalties only reinforce subdermal armor as impractical.  Also as reinforcement, it is not quite a "layer" of armor.  By the same logic your natural Bone structure should offer some sort of SP rating and count as a layer.

    Working Skinweave & Subdermal Armor:
    Remember, there are PLENTY of areas NOT protected by these forms of protection;  Genetalia, palms, eyes, mouths, nostrils, ear canals, rectums, etc. are not protected by skinweave and subdermal armor declares that it only protects the torso or head.  These areas gain NO SP rating aside from worn armor.  Also, remember, to reach subdermal armor, the atack must reach, or break, the skin.  The target takes 1 point of bruise damage automatically (then total up the damage as per normal).  Skinweave is handled the same way, except only half SP applies to blunt attacks (gel and rubber rounds apply here).

    Armor Layering:
    Oh boy, here's the big boys here.  Layering rules, as they apply now, they sound good, but what about layering of reinforced clothing?  Well, it's okay to use the rules they give you, except if you start to account for fashion.

    How Much is too much?
    So, you decidedto ditch the stormtrooper look for something a bit more socially acceptable, GOOD!  Now, let's get down to buisness.  For much of this, I'll be using my character for examples and as a template.  I'll go through this ensamble, and explain everything along the way.
    First, Trax's enhanced with SP 6 rated skinweave.  Why?  It's no good to have so much OBVIOUS armor that you look paranoid or afraid.  SP 6 is the lowest possible rating he could get.  It offers enough protection that he doesn't have to constantly lug an armored jacket around in the Night City heat.  Skinweave, when he needs that extra bit to cover his bets.  Skinweave, so natural even your lover can't tell.
    SP 6 pants, because if you break a sweat lifting your legs to walk, you are going to pass out when you have to run someone down.  The SP 6 pants combined with the skinweave offer enough protection as lightly armored pants.  SP 6 is enough that it is socially acceptable, almost everywhere, and relatively unnoticable, and resiliant enough to take a bit of punishment before having to be repaired, or replaced.
    An SP 4 T-shirt gives Trax's upper body the protection equal to a kevlar vest, but isn't even half as obvious.  Being that the article is a T-shirt and the SP rating is one of the lowest on the market, the shirt is appearing as a normal t-shirt unless looked at closer (NEARLY IMPOSSIBLE to notice that it is so much more).  The T-Shirt is light enough to not inhibit movement and lets Trax's skin breath like a regular T-shirt (Aren't anti-ballistic fabrics great?).
    The SP 12 Jacket might raise an eyebrow or two, so permit me to elaborate.  First, note that this is the heaviest he wears REGULARLY (though the SP 14 Trench is heavier, it isn't worn as frequently).  Second, let's consider the clothing today.  How hindered is our movement by a T-shirt?  Answer: not very.  We can move pretty easily.  If we threw an overshirt or flannel on top, we are still unhindered.  When a Trenchcoat is worn, much bulkier than a majority of jackets, even leather jackets, most are only hindered by the weight, and the bulk of something as already light as a lightly armored jacket to a man with a body rating of 13 (well into superhuman) is going to be MUCH less than if the same jacket were placed on a person of body rating 7 (average).  And the Jacket (which is a bit more obvious than everything else) also serves to let people know that  he is concerned with his protection.  You see, if he was conceiling all his armor, people would suspect that something was up, this helps to extinguish some of that.
    Now if Trax put on a flack vest or even metal gear over the armored t-shirt, I would still apply ONLY the penalties the armor has itself.  However, if someone attempted to put a HEAVY ARMOR piece on over the jacket (even with no T-Shirt underneath), I'd apply a small layering penalty.  Why?  Because think how hard it is to move in a life preserver vest, over a thick piece of clothing.  Moving in a Flack Vest is like that.
    So layering penalties should apply as a mix of what the clothing type is that the armor is built into, and the thickness (the rating of) of the armor.  The lower the number, the thinner the clothing is (and less obvious as a protective garment).  This does not permit the character to wear five or six SP 4 t-shirts with no penalty.  And for concerned GM's, remember, anything the characters can do, the street trash can do too.  So don't dress heavier, dress smarter (and for G-d's sake! USE COVER!)