Senna, Sorry to hear about your son's issue. Have you had his shoulder range of motion checked? This may sound weird, but if you lack shoulder mobility, mainly extension, it is harder to get into layback when you throw. That means the throw becomes more pushy, and then the tricep has to take over/has more stress placed on it. I was having a ton of tricep tightness after I pitched, and finally saw a PT who tested my shoulder mobility and then gave me the explanation above (Definitely more technical than how I just wrote it).
Obviously this isn't 100% what your son has, but if all the scans are clean there's a chance it could be. For me as I started to gain back the shoulder mobility the problem has started to dissipate. If you have any video of him throwing , you may be able to see that he leads with the tricep. Personally I would suggest trying to get in to see a physical therapist who deals with a lot of baseball players. They'll probably do a bigger screen, and may find the problem, or at the very least have some exercises or treatment that can help to make sure the pain doesn't come back.