Widest part of the body is the best measurement for prey size. The neck is super stretchy and the jaws will open way further than you'd think.
I suspected since the vet wasn't concerned, it was just the spurs. Since some people think they're part of the sexual organs(because that's what they're used for apparently, to poke at the partner snake), the vet probably just used the wrong term. Even a experienced vet can have a "brain fart" and use the wrong term.
Ball pythons are super tough and can rebound from things easily. Once he is eating the right size prey on a regular schedule, he will probably grow very nicely.
Just as a caution though, sometimes animals that have not been fed properly will die later on, due to organ damage. There's not really anything to do to prevent that risk at this point and it's not really your fault since you had people telling you that all was well. Just don't try to push too much food to grow him fast to "make up for" the slow start. Let him grow slowly on a regular schedule.
Everyone was new once. Don't sweat it.