Your child is with you more than anyone else, and you're the one giving the most supportive, loving care (resulting in happy responses), and the most frequent controlling demands (resulting in unhappy reactions).
With the latter, your son learns to expect your demands to be frequent and frustrating, so he has become very sensitive to that dynamic, and his reactions are quick and strong. Particularly with the PDD-NOS: The children with PDD-NOS "are able to show joy, fear, or anger, but they may only show the extreme of emotions." (from http://autism.wikia.com/wiki/PDD-NOS).
So you probably get unhappiness, magnified, when your son reaches his emotional tipping point. And when you and your son are with others in a clinical setting, you probably behave toward him in a somewhat different manner – many of your expectations have been suspended in favor of the professionals' agenda. It sounds like he just doesn't reach the same degree of repetitive frustration as he does at home.
Even without that diagnosis, a child hitting himself (or others) is not an uncommon behavior. My grandson did this occasionally between the ages of about 1 and 3 – either when he was feeling wildy frustrated or unfairly corrected. In his case, the theme of "unfairness" was the common thread, and I expect this is probably true of other kids as well, since fairness and justice are HUGE features in a child's inner landscape.
If you'd really like your child to have fewer of these breakdowns, which are a form of tantrum directed against himself, there are two things that are known to be helpful.
First, don't add any emotional reaction or upset of your own to the situation. Make him safe and perhaps hold him gently but firmly until the spell passes, but don't act upset or alarmed. He needs your steadiness when he's lost his. If you don't hold him (hug him firmly but not punitively), you might try this, and find out whether his episodes end faster. Sometimes kids who are wrapped up in a hug seem to feel safer, and surrender to the caretaker's love more easily.
Second, train yourself to be sensitive to the circumstances that trigger his reaction, and to whatever degree possible, establish a more positive approach. Toddlers (particularly with nervous deficits) have little impulse control or ability to draw working conclusions from alert observations, but presumably, adults do.
So changes from your end might include things like adjusting your expectations if they're not totally age-appropriate, giving him advance notice of upcoming changes ("bath-time in five minutes, so finish up what you're doing, okay?"), easing his schedule, and your own, as much as possible so he doesn't feel rushed, manipulated or controlled as often, moderating your tone of voice (giving polite information rather than an impatient command), breaking your expectations into smaller, more concrete orders (instead of "Pick up your toys!", perhaps he needs, "First, put all the little things in this basket…").
For yourself, I also suggest learning to pay attention to your own breathing when his episodes are loud and long, remembering that he gets through them and is cheerful again, and knowing that he really can't help a great deal of what he does. His self-harming behaviors are, to some extent, just part of being a toddler, and his may be exacerbated by his neurological deficits. It's good that you want to find the healthiest possible way to deal with this.