Hm... my younger sister has Celiac's, Asthma, allergies, and a few other things, but she is definitely not Autistic (although, she doesn't seem neurotypical from my observations, perhaps some form of ADD/ADHD would be my guess). My mother also has Celiac's, Asthma, allergies, Lactose Intollerance and a few other things but she is neurotypical.
I definitely have Asperger's but no Celiac's, Asthma, allergies, or anything else... Although, I used to have bad stomach pains when I was younger, which, in the 10th grade actually caused me to throw up (intense pain -> dizziness/hot flash -> I run out the classroom). I suspected Lactose Intollerance, and began to avoid drinking milk (especially at school) because it seems to exacerbate the stomach pain (which weirdly, lessened as I got home from school).
More recently I've had a few seemingly acid reflux-ish problems. I'm sure this all is/was just a product of my diet at those times (pizza!!). It's been a while since I've had either problem though, probably because I don't eat much nowadays...
I apoligize if any of the conditions I mentioned aren't Auto Immune, I wouldn't know. My only diagnosis is Asperger's, while my mother and younger sister have other conditions (auto immune and not). My elder sister who is neurotypical shares none with my mother and sister, in addition, has no other conditions (that I know of)