I'm sorry, I'll try to not sound like a jerk, but my line of thought may be too objective right now.
In my crude opinion the majority of ppl who posted photos here were never ugly....
I know you put up with a lot, however, I think the OP is referring to another level of ugliness. The level that doctors think she has some kind of syndrome.
This is a girl that showed up when I googled for Apert Syndrome.
I would resource to some church... I'm not religious, far from that, but I frequented a few churches, because my friends and family would too. There, we always had contact with people with some kind of abnormality (again, not trying not to be an asshole, just using the original meaning of the word) and we got used to this situation.
At the start, I thought they were ugly as hell (yeah, I were a jerk, I was 9yo...) but then they started to look normal to me. Not beautiful, nor ugly, just normal. As when I looked in the mirror and thought: "huh, normal...". I liked them. No matter what, they were always the cheerful people, kind and, most of the time, funny.
After a few years, and a lot of reflection about life, I still classify the world as ugly and beautiful, because that was the way I grew up. I guess we were coded to like beautiful things and person, but the ugly ones, are just another interpretation of what beautiful mean. As you said, she IS beautiful, just in her own special way. Someone else will see it too, your job as parents is to never let her forget that. And I think that in the church (or another group that is benevolent, can even be some friends at the school) you will have a lot of help too.
About doing something about her looks, ask in some kind and subjective way, if she wants to wear cute clothes, or do make up. Or else, she will notice that you, in your eyes (not your heart) don't think she is pretty. If she agrees, you could try to focus on clothes and hair, and a light make up. Don't put much make up on her "faulty" parts, because it will get too much attention, I guess... I dunno, I'm a dude.
/u/Zifna gave an answer so much better than I, still, read everything people answered, even the ones you don't like.
