Well, they're both unspecified codes.
K59.9 is a functional disorder, not a disease, of the intestine.
K63.9 is disease of the intestine, not a functional disorder.
A person might have a condition in which the intestines are not functioning properly, but that doesn't mean they have an actual disease. And a person might have an intestinal disease, but that doesn't mean the intestines are not functioning properly, although they could be due to the disease.
Think of it like this: a person might have pain and stiffness in their joints, but that doesn't mean they have arthritis. Likewise, a person might have arthritis but is taking medication or other treatment and the pain and stiffness aren't flaring up.