Hi T.,
Our boy was diagnosed with torticollis at twelve weeks also. The right side of his face was quite flat in comparison to the left, and now, at age three, there is a slight difference. The pediatrician and EVERYONE else tells me that they don't see the difference, so I'm just paranoid.
Anyway, what we had to do with the sleep positions to help even out the growth of his face was to put him on his left side. We used bolsters, and literally tucked in a blanket to keep him on that side when he slept. Doing that and the PT slowly corrected the problem. He really hated the PT, not because it hurt, but because the therapist had to sort of 'man handle' him to manipulate the muscles and ligaments. I cried the first session because I felt so bad for my little guy. One thing that really helped was to hold my boy in my arms so that he was lying on his 'good' side with his head SLIGHTLY elevated above his shoulders. This position helped stretch him, and he didn't seem to mind it as much as some of the other stretches.
I don't know how severe your son's case is, but rest assured that it is a totally treatable condition and he will be fine. If his case is severe it is likely that you will end up having him in helmets to even out the growth of his skull bones. We didn't have to do this, but from what I read on the internet, it is a successful therapy.
As for why it happens? Unknown. I theorize that my boy's happened because he was head down for the last 9 weeks of the pregnancy. I'm a 'mature' mother and had to be monitored twice per week for the last nine weeks. That monitoring included a weekly ultrasound which showed him head down, ready to go!
If you want to send me a private message, I'd be happy to send you a photo of the side-lying position that helped us so much.
Your precious will be fine.