We had a screen-positive antibody for celiac disease shortly after my son’s T1 diagnosis at age 11. Once we got our feet under us with the T1 diagnosis, we eventually had a consultation with a pediatric GI who specializes in celiac (we’re at an academic medical center) and eventually scope and biopsy. We have a persistent low titer positive antibody and mild focal changes diagnostic of celiac on gut biopsy. My son has zero GI symptoms, no anemia, no vit D deficiency, and has pretty much topped out his puberty growth spurt (5’7’’ and 140 lbs of muscle at age 13). His BG control is also quite decent for an adolescent. So we are in the wierd position of having to decide whether to treat (ie adopt a strict GF diet) despite no evidence the disease is hurting him. Our GI says this is an area of uncertainty–the literature on consequences of untreated celiac is scary, but it’s mostly from adults who went untreated (some with symptoms) for many years, not kids picked up by routine screening who have low titers and mild changes. There’s a Canadian study randomizing kids like mine to GF diet or not, but it’s not complete yet. We have “mostly” concluded we will wait at least a couple of years before adopting the diet, mostly because we think it would be very difficult for a teenager to adhere strictly when gluten doesn’t make him feel bad, and we’d rather he focus his self discipline on good T1 control which we KNOW has big consequences rather than something else with less certain benefits. Plus, hey, we like donuts as much as the next guy 
. But we’re experimenting with minimizing wheat and making new meal habits with other grains so if the change needs to happen, it won’t feel so dramatic. Anyone else out there with screen-detected “silent” celiac? What did you decide to do?
I have celiac. One thing in particular stands out in your post:
Even if he doesn’t have symptoms or apparent nutrient deficiencies, the disease IS hurting him. There are changes to his gut - that is, damage to his gut - from the antibodies attacking his body. This will only continue as he continues to eat gluten. I’m not sure at all why your GI doctor would be on the fence about a GF diet. 
When I was diagnosed, I (thought I was) asymptomatic. My sister, diagnosed at the same time, also didn’t realize she had any symptoms. Once we cut gluten out, though, we noticed immediate improvement in our health - things we had dismissed as “normal” - and we had the typical symptoms after accidental gluten ingestion that everyone talks about. This could possibly be the case with your son.
It’s also likely that he is just a silent celiac - there are a small number of people who never have symptoms, as odd as it seems considering the damage being done to their small intestine; surely they must have symptoms! But they don’t. I cannot imagine how difficult it would be to adhere to a strict celiac-safe GF diet (which is different from just a standard GF diet) when there are seemingly no consequences. The problem is, there are consequences; it’s just that he will see them down the road and likely far too late to reverse some of the damage.
I am so sorry that y’all are going through this. If you have any questions about celiac disease/GF diet, I’d be happy to answer them. There are a couple folks on here with T1 kiddos who also have celiac disease who may be able to chime in as well - @Thomas and @Aaron (I think?).
@katiereeder, I feel for you. My son was diagnosed about the same time, and thankfully hasn’t been diagnosed with celiac as well. that is quite a 1-2 punch.
Personally, I would remove gluten for 2 weeks and see if he feels better. Then make a more permanent decision.
I equate this to a decision my family had around dogs. My wife had dogs her entire life, but tested positive for dog allergy, she honestly had no idea. Once our last dog died, we said if my wife didn’t get better in 6 months we would get another dog. The upshot is she felt a lot better and we haven’t had a dog since.
@katiereeder - My son has celiac as well but it is very symptomatic so we just went GF without a second thought. His symptoms showed up about 3 months after his Type 1 diagnoses and he had a very high antibodies.
I realize that I am probably better with change than a lot of people, but so far we have managed to eliminate gluten and replace it with non-gluten alternatives. The only real pain is what @Pianoplayer7008 says about the celiac-safe GF diet - it can be a pain to be 100% sure there is no gluten in a product that does not appear to contain any gluten.
I am going to do gluten free yorkshire puddings tomorrow with dinner to see if they are ok. Finger’s crossed. Maybe next I will do GF doughnuts… (CARBS! 
)
Yikes… I had not zero but not high enough to be a positive antibody level for both thyroid and celiac crap. Fingers crossed I don’t get another full blown autoimmune ******.It’s monitor every few years or if symptoms develop for me…