I have had two dogs whose skin tuns black. When it happened to the first dog I asked the vet about it and he said it was nothing to worry about and it sometimes happens. Now it is happening to a second dog. The skin doesn't stay black. It changes sometimes during the day. It is on the tummy area and groin. I never notice any itching specifically in the affected area. Both dogs have had allergies as well. There is never any other change in the skin, just color. I have not asked by current vet about it because of what my previous vet told me but I though I would check the internet to see what other people are experiencing.
How does the rest of his coat look? Has it changed from healthy, shiny and thick to something less than that? Is he scratching more than usual? In good health otherwise? Is the black area usually covered with hair, or did the hair fall out as the skin changed color. How long did it take for the color to change, and has it affected the same amount of skin, or did it start small and grow from there? How fast?
Allergies are a great place to start, but I agree it can be time consuming and frustrating to stick to a novel protein elimination diet to figure out exactly what is causing the allergies. That is a common enough reason for skin discoloration, but since you don't mention any other symptoms like itchy and scaly skin, the problem is perplexing. The only other thing I can think of is hypothyroidism (low thyroid) but I think that causes overall discoloration instead of patches. Something to ask your vet about anyway. Cancer would be another consideration, but your vet obviously doesn't think this particular area qualifies as any kind of cancer.
Because your vet was wise enough to admit she hasn't seen this in her practice before, it would be reasonable to ask for a referral to a canine allergy and dermatology specialist. If you live in or near the Houston, TX area, I can personally recommend Gulf Coast Veterinary Associates. They have the same kinds of specialists for animals that you would expect in human medicine. Of course, they aren't cheap either! A large university with a veterinary program is another option for specialized care.