I found a 3D outer-flesh model and a 3D "High-Poly" skeleton model and merged them. The "Medium-Poly" and "Low-Poly" skeleton models changed the shape of some of the bones, so I used the best-quality model. This meant a large file size, so I removed some unnecessary bones. This does not affect where the bones in the upper body appear in the model.
I'm showing how many facets are involved in the "High-Poly" skeleton model and the articulation "handles" I added. Using the "handles", each articulation point can be rotated (to a reasonable degree; some joints don't rotate much) but the articulation points themselves remain attached to the articulation point of any neighboring bone it was originally attached to. For example, one can rotate the skull but it can't be detached from the C1 (or "Atlas") vertebrae. This preserves the integrity of the skeleton.
The scapula bone is very flexible and attached to the back by large muscles. The scapula has a connection to the outer tip of the clavicle. When the inner tip of the clavicle is rotated upward, the outer tip of the clavicle rises which in turn causes the scapula (and arm bones) to rise up. I think we see in the autopsy photos that the outer shoulders of Kennedy have risen up due to rigor mortis. The raised shoulder line is fairly flat in the photo, compared to life where the shoulder line tapers down from the neck.
On my model, the distance between the neck crease and the entry wound on the skin is 2 1/8" (or 5.5 cm as reported by the Clark Panel). By raising the scapula up, we end up with a similar distance from the scapular spine to the entry wound. Those two distances being similar is what is shown in the autopsy photo of the back wound. A resting scapula would not appear as high as that seen in the autopsy photo.
I notice that young Kennedy's right clavicle protrudes from the body more so than the left. I think I see something similar in the autopsy photo, which helps to authenticate the photo.