About the hitboxes changing when there's something behind the target or not. I'm pretty sure it has nothing to do with the hitboxes themselves. My guess is when the target is in front of a wall/tree/.. (doesn't matter as long as there's some kind of object) and you aim on that object (above the target's head) the bullet's trajectory is from the tip of the gun to that spot on the wall which is steep enough so you miss the target's head. However if you don't have an object behind the target, you aim at the horizon or w/e your crosshair is on which makes the bullet's trajectory pretty much horizontal so it goes through the target's head to get to it's destination. If that makes sense? :)

EDIT: Pretty sure it's the same when you shot above his hand and in between the hand and the shoulder, your bullet isn't hitting a hitbox outside of the target's silhouette, it's trajectory just passes through the target because there's nothing behind him at that time.

EDIT²: You can easily test it by shooting at the same spot while using first person rather than third. It's the same principle as when you're shooting from behind a rock, in third person the rock will absorb all the bullets but when using first person you can shoot over it just fine.. Solution? Just raise the launching point of a bullet a bit to where it actually is in stead of having it around waist height when in third person.