I have found that audiosensitivity ("hyperacusis") in the general population, ENT patients and in autistic children is of peripheral origin, detectable by abnormal stapedial reflexes. Specifically, thresholds are lowered at some frequencies to 70db and/or reflexes are reversed, ie a momentary, however slight increase of compliance at onset, as opposed to the normal decreased compliance or increased stiffness of the ossicular chain. The likely cause for this is middle ear dehydration leading to reduced perilymph pressure and resultant endolymphatic hydrops. The most likely cause in a 3y old would be over-aeration of the middle ear, as with a grommet or patent E Tube.
Unfortunately we do not have information on hypersensitivity, but the possibility of a change in the growing stages is interesting. Expression of the origin of the trigeminal ganglion may be involved.