How do tissue layer positionings work? Typically nails are added to creatures using [TISSUE_LAYER:BY_CATEGORY:FINGER:NAIL:FRONT], but does that mean they're getting placed on the tip of the finger, or the back? It could be either one, depending on what "FRONT" is supposed to mean (and in real life, technically it's both at once in a way?), and "FRONT" is ambiguous because it depends on what position their hands are supposed to be in (are they T-posing? Are their hands forward like a zombie? It's not clear at all!).
The same question extends to other body parts that can have ambiguous orientation, like the arms, hands and legs. Pretty much the only part I'm clear on the meanings of is the head, where clearly FRONT is the side the face is on, and the TOP and BACK and all that are based on a humanoid head facing upwards. The body is also kind of clear for the same reason (so TOP would be where the neck is, even for quadrupeds where technically the part on top would be their back).
Also, how do tissue layers interact with internal body parts? I don't see what it is that lets guts know they should be behind the skin and flesh, but not behind the bone, since the wiki says [INTERNAL] means:
"Marks the body part as being inside the body. It is behind all the other tissues of the body part, cannot be severed, nor used for wrestling. It cannot be targeted directly in combat, but can be damaged by attacks to the parent body part.
But it doesn't seem like attacks have to go through/cause damage to the parent body parts bone tissues in order to damage the internal organs? What am I missing here?
It's best not to think too hard about what DF creatures actually look like. There are rules for how combat calculations are handled, and outside of those it doesn't really matter.
All body parts are basically magic floating spheres. Therre is no real logic for how they are connected to each other, apart from impacts applying force further up the tree and severed/damaged parts causing parts further down the tree to be lost or stop functioning.
I believe that the positioning of tissue layers may affect the likelihood of that layer being hit when attacked from a particular side - so FRONT means you are more likely to hit it when attacking an enemy head-on and BACK means you are more likely to hit it attacking from behind. Relative position and angle of body parts aren't really relevant.
Attacks on internal organs do need to pass through all tissue layers. It is worth noting that vertebrates do not have an internal bone layer on their torso or head. The skull is simply an internal organ classified as being AROUND the brain. This means that it is very possible to hit the head and miss the skull - tissue layers are always hit unless blocked by a higher tissue layer, while internal parts are hit at random - but it is not possible to hit the brain without going through the skull.
Ribcages are even dicier - each individual rib is classified as partially AROUND the lungs and heart, which means that it is possible - though not guaranteed - that attacks to these organs will be intercepted by a given rib. And spines are just independent organs, not actual layers. In fact, if you make the spine out of adamantine, you can still cut the body in half with a steel axe - the spine has no role in holding it together.
So basically, upper and lower bodies are just big hunks of meat with organs and bones floating around inside them.