Unfortunately, I can't really give you a definite diagnosis as to what this is but I can give you a few thoughts that might help.
First, I agree with the endocrinologist that this does not sound like insulin resistance. Insulin resistance gives a classic hyperpigmentation rash called acanthosis nigricans. It classically is located on the back of the neck, and the finger joints. It would be very unusual for this to present as you have described.
John has suggested Addison's disease, which definitely can cause hyperpigmentation and can show up at this age. It may be worth checking a cortisol level, although I would expect that the hyperpigmentation of Addisons should be more diffuse and symmetrical. This is because in Addison's disease, the brain is making extra ACTH to try to stimulate the adrenal glands, as a byproduct, the melanin glands are also stimulated to produce more pigment. This effect is global so the pigmentation changes should also be throughout the body.
One possibility is a cafe au lait spot, although it really doesn't sound like this to me. A congenital nevus can look this way but I'm less familiar with these showing up so late.
I would recommend your son see a dermatologist. If one is not available, a skin punch biopsy of the area may provide some answers as well. Again, I think going down the endocrinology path is unlikely to be of help. However, if this is continuing to be a question, doing a fasting insulin level or c-peptide level will answer this for you. If it is normal, this is not related to insulin resistance.
Advice and opinions given are based on the information provided and must not be considered an official medical recommendation. The limitations of the internet prevent an appropriate evaluation. Always consult your doctor if there is concern.