If I am not mistaken, this article is more than a little sarcastic. The naming of "Dr. Protractor" clues you in (remember that a protractor is a tool with which to measure and create angles), and then you can work from there.
People with autism have no distinctive facial features. The only distinction I see between Auties and non-auties is that auties tend not to like using make-up as much, and do not follow trends when it comes to hairstyles and clothing, choosing comfort instead. Some, especially Aspies (including, in the past, me) have poor personal hygiene. So the perception of ugliness may exist despite the reality that our facial features represent the human norm pretty well.
Aspies may tend towards being either overweight (from a sedentary lifestyle) or very thin (from forgetting to eat or having extreme food preferences), neither of which is attractive. However, these have nothing to do with how regular one's facial features are.
(Sometimes autism occurs along with a congenital disease that does change appearance. This would be the exception to the rule.)
Personally:
--I never use make-up
--I'm overdue for a shower, having had my last one the day before yesterday (and planning to take another tomorrow morning)
--I cut my own hair; right now my short hair is a grown-out shave from last summer
--I'm 60 pounds overweight
--I wear clothes for comfort, usually khakis and T-shirts, without bothering much to match them
--I never wear jewelry other than very small earrings and a blue bracelet (which has symbolic meaning to me)
--My shoes, which I hate wearing at all, are always sneakers or tennis shoes, for maximum comfort; or else, in summer, flat sandals with wide leather straps.
All those things, despite my average face and good complexion (not being especially prone to acne), probably take my appearance down quite a few notches in the NT mind. Because NTs are not likely to distinguish between what someone looks like and the accessories they use to enhance their looks, they may see a general "ugly" appearance where one does not actually exist.