Can we see photos of him?
Is this an exotic specialist vet? It doesn't really sound like it if they have no idea on how to help...
Honestly the only time a ball python should be hefty or thick is breeding females or growing babies before a growth spurt.
A lot of people let them become obese.
And while I agree that he sounds very small for a 3 year old, it's still something that it's better seen than just agreed upon.
And the 'largest males eat small rats' always amused me because my oldest male outsized and outweighs all of my
females currently at over 3000g and almost 5 feet long. He gets a medium every 2-3 weeks. Hahah