I'm sorta now saying I don't believe he did. Because if he was stuck in that in between form and if it's all a one piece metal type deal... how does he get out of it. That an later he gets wrecked by Dr. Light...I think... and he looks almost all machine except for maybe his head.
But again, the whole penis avenue is not that huge of a deal. It's just his mid-torse and head where the traits that made him the most Human. Those physical traits made him and everyone else the most vulnerable. I think those traits are essential to the human half of him and set him apart from the Robot characters we were talking about before.