Sometimes there are two “separate structures” that function interdependently. The neck and shoulder are a perfect example of this. Whether you are looking at musculature, neurological structures, or other factors such as lymphatic drainage or even parasympathetic innervation, the neck and shoulders generally look similar or at least share much of the same anatomical space.
The brachial plexus originates from the spinal cord in the neck and then exits through the armpit before travelling down the arm. This means that 100% of the nervous tissue in the upper extremity originates in the neck and passes through the shoulder. So, one can only imagine how they can have an effect on each other, whether positive or negative.
Lymphatics from the upper extremity both drain into the brachiocephalic veins which are located between the first rib and clavicle (collarbone). This is essentially the region where the shoulder meets the neck, so an issue with either one may cause symptoms in both because of the shared anatomy.
In terms of musculature, many muscles have an origin and insertion that spans from the neck to the shoulder. When one of these regions is dysfunctional, the other is bound to have issues as well since many of the same muscles are involved.
Another key component to this is positioning of the shoulder blade. By strengthening the periscapular musculature, you are putting the shoulder blade in the best position to function. Since one end of the shoulder joint is part of the shoulder blade, this has a massive impact on the shoulder itself. The shoulder blade also sits on top of the upper ribs and glides upon the ribcage as the shoulder moves. If there is pain or dysfunction in the neck, it can have an impact on the scapula through connections such as the trap muscles and alter the position that the shoulder joint ends up in. For this reason, strengthening muscles like the rhomboids and lats is of huge importance for neck and shoulder function.
Moral of the story: don’t think of the neck and shoulders as separate entities when you are experiencing pain. If one of them hurts, address both.