Ok so fist I will start with the basic not so confusing stuff the neck seams I always wondered why these existed then I thought this was because these were two different models attached this also answers why arrows that hit people's heads appear in the chest but the once I was messing around and I killed an npc and then shot an arrow at his head and it appeared on his head so my model theory must be wrong,right?so I was wondering what is up with these npcs?and afterwards I used the console to resurrect him and the arrow stayed on his head.

Very few people have any insight into the underlying game engine which is almost certainly what controls where arrows appear. Head shots simply have no special significance in the game although I wouldn't be surprised if some modder takes this opportunity to promote a mod that does just that. If you are on a PC, I think there is a mod that cleans up the obvious neck seams.

Shooting or getting shot in the head tends to result in shoulder or torso placement of arrows in combat.
Were as afterwards it imbeds into the skull, I allways presumed this was due to living ( or at least animate ), models having many moving parts in the face...
Mouth, eyes hair, and the placement would either be ignored their due to an issue of bugs, or a refresh being caused when the face / head / eyes change position.
This of cause is just what I allways believed, it will take someone with more knowledge to give the right answer.

I always thought it was because it would be ridiculous to see someone with 30 arrows sticking out of their heads running after you and so they made the arrows magically appear in the torso area.

I dunno... here's my observations as a master marksman on the 360: For example, out of say, 100 different human kills I make, where I am aiming for the head (almost always aiming for the head), 97 of of 100 times, my arrows will appear in their chest. But I have definitely made many one-hit kills where my arrow appears in their head. It's always a single arrow, never more.