Sometimes if you do not have the genes for celiac, which in the United States are DQ2 &/or DQ8, you might not present with typical celiac symptoms. You could have atypical symptoms & be gluten intolerant. When a person has gluten intolerance they will usually suffer other autoimmune illnesses and symptoms that can affect any organ of the body. If you have any of the following neurological issues such as, migraines, depression, ADD, ADHD, dyslexia, seizures, bi-polar, Schizophrenia, etc you probably have at least one gluten intolerant gene.
Of course just to make it a little trickier you can have two gluten intolerant genes & test postive via blood tests and/or biopsy. But usually that is not the case. From my observations the chances of having a positive celiac test with gluten intolerant genes go up as you age and if you have more than one or two autoimmune issues.
Those of us that have gluten intolerance the gluten free diet keeps us healthy & happy. For some of us the whole body can fail us and the villi are still not flattened. All the while we get a complete recovery on the gluten free diet.
I tested thru Enterolab.com and found out that I have 2 gluten intolerant genes, double DQ1. At least I have different copies of the same gene. If a person has two copies of the exact gene, one from each parent, usually their health is worse that a person that has two different genes.
A friend that I write about sometimes that had Crohn's, tested thru Enterolab & she had a DQ8 & a DQ2! she immediately went gluten free & was better on about day 4! I think that she now tries to get the word out to the people with Crohn's.
In summary, IMO just because you do not have flattened villi does not mean that a gluten free diet will not help you.