I doubt micropenis is the case after having a circumcision. The doctor would identify this, and previous doctors should have noticed by this time.
He may have retractile penis. This is where the tendons act like elastic bands and pull the penis in towards the body. A large portion of the shaft may be hidden in the body, whereas his peers may have the shaft full hanging out. His penis may only fully or partially emerge when erect.
There are surgeries to correct retraction penis if you believe it may cause humiliation and feelings of inadequacy. I am going to a paediatric urologist for another visit for my 3 year old to see if we should correct this now. He too had a circumcision and his penis seemed to retract after that and never came back fully. I don't know if it is related, but I can tell you the condition is more common than we know.