It sounds like you are describing discomfort in the brachiallis muscle. Given the tendency to short arm as you describe this is predictable, and this is a very common problem. The fix for this is teaching handbreak in a different way so that the arm ends up longer in the back and gets the ball up slightly BEFORE the stride foot plants. If you want more definitive info send me a PM.
I worked with a HS sophomore on Sunday (tremendous athlete who’s already 6’4) who does the same thing as your son, with the same consequence. He learned what to do differently in the space of about an hour and his arm was feeling much better.
Best wishes to you and your son.
Edited to add: Roger is correct that the ‘football’ pitch is a breaking ball…this is the beginnings of a slider where his hand is coming around the outside of the ball. This adds to the elbow discomfort you are describing and is a distinct no-no for youngsters.