(I'm not a doctor or even a scientist at all, I just sometimes get into speculative biology.)
Headcanon: The Werehog has hyperpituitarism.
When transformed, Sonic visually shows signs of gigantism and acromegaly, both being caused by an excess of growth hormone before and after epiphyseal closure (bone growth plate fusion) respectively, and hyperpituitarism is usually the cause of excess GH.
The gigantism is simple enough. Sonic gets taller, and for a hedgehog at least, he gets huge. Going from 3'3" to 4'1", Sonic's height is increased by ~26%, and in human proportions, that would be the equivalent of someone going from 5'6" to 6'11".
The acromegaly is likely what gives Sonic his more distinct features, such as the thicker brow ridge and more pronounced facial features. His larger hands and broader fingers would be caused by thicker joints and soft tissue swelling, which the latter of can also cause a deeper voice from thicker vocal cords.
But having both gigantism and acromegaly would imply epiphyseal closure occurs during a transformation, which...ouch. I get the feeling it'd make the second half of it more painful, if it wasn't for him instantly changing, that is.
On a lighter note, Sonic basically turns into an anthro equivalent of Andre the Giant at night.