My DS1 was diagnoses coeliac age 4 - similar symptoms to your son and with hindsight he'd had it at least 2 years.
Irritability is a known coeliac symptom. My DS age 3-4 was quite highly strung, easily upset / flew off the handle. Two years of gluten-free and he still has those tendencies, but considerably reduced.
Interestingly, he also had a strep throat problem after diagnosis - ours went on recurring every few weeks for over a year. Each time he would be absolutely wiped out and exhausted by it, and very irritable. Eventually a doctor worked out that it was being passed back and forth between him and his brother, and gave them a simultaneous long course of antibiotics which cured the problem. Now on the rare occasion either of them gets ill, they're not irritable with it and not exhausted either.
You should be getting regular (6 monthly or annual) blood tests for your son to check the gluten antibodies. In refractory coeliac disease, these will still be high despite a gf diet. If the antibodies are reducing (and they should reduce to zero within a couple of years) then you don't need to worry about that.
I don't know how bad your DS was at diagnosis. Mine was level 3c on the Marsh scale, so very badly affected. The gastroenterologist said it would take 2 years for his body to recover. His last blood test (at the 2 year point) showed a slight positive for antibodies - hopefully at the next one that will be down to zero.
It can take a long time for full recovery from the villi damage, and I think that until then, any illness can really wipe them out because they're still not absorbing the full amount of vitamins etc. to help deal with the illness.
I don't think your DS will have refractory disease if you saw improvements straight away - it is more likely that being ill is sapping his energy.
Hopefully in 2 years you will have the same feeling as me - every time I look at my strong, flat-stomached, bounding with energy, full of enthusiasm DS, I feel so grateful that we got the diagnosis when we did, and transformed his childhood.