How are celiac disease and autoimmune hepatitis different?

Totally different: While both are autoimmune diseases, celiac is basically a GI disease characterized by a sensitivity to wheat (gluten) and hepatitis is characterized by inflammation involving the liver.

The target: Most would understand that the antibodies you develop after a measles shot attack the measles virus, not the flu virus. In the same way, the antibodies that develop in celiac attack the tissues specific to the intestine and not the liver cells. Autoimmune doesn't mean the whole system attacks itself, it is usually quite specific to the target selected.