That paper is very specific to very early onsent IBD. Low NADPH makes sense for sure, but maybe not in the context of this paper. Main reason being, you can't fight off pathogens with low NADPH oxidase. It's sort of like the low HLA MHC Class II gene variants in MS - you can't fight off the pathological infection because antigen presentation is poor, so the body develops a pathological infection that gets labelled as an autoimmune problem (in MS, the culprit is EBV).
For IBD, several strains of pathological bacteria and fungi have been identified as primary drivers of disease process, and one problem is that they develop into very strong networks sustained by biofilm, and they become impermeable to antibiotic and antifungal treatments. NADPH oxidase is central in degrading these networks and fighting off the initial infections, and without it, they can proliferate and cause a sustained immune reaction. For very early onset, this makes a ton of sense since environmental conditions have much less of an impact because they take time to have an impact. For cases when people develop it later in life, it is probably a different issue - but it could potentially share some things in common.
I'm moving over to much more of a infectious disease and environmental focus for autoimmune diseases myself. I think the cycles the immune system gets into are too difficult without some serious stimulus from environmental toxins and the local infectious ecology. When paired with the right genetic conditions, some kind of environmental toxin, stress, and an opportunistic infection, you get what looks like an autoimmune process. I think fixing minerals can improve these conditions, because they simply allow the body to self-regulate infections a bit better. The high copper you show in hair could just be a result of your body fighting off a bacterial or fungal infection, since copper is an antimicrobial agent. As you put new minerals into your system, feed the healing system, and achieve balance, your copper comes down - not because you're chelating it, but because you're removing the demand for it. I think the body is much more of a reactionary and thinking system that can react to things with the sensitivity and speed that we don't even have the capacity to detect yet. But it reacts to things that are essential, often at the cost of other less important demands (ie, sacrificing reproduction for survival, or sacrificing digestion to fight off an infection).
Why is calcium high on a hair test? Probably because the body is probably trying to stimulate respiration, so it lets calcium flow from the bones and into mitochondria to stimulate respiration (and as a result, things like respiratory rate). It probably detects that metabolism is too low, so it wants to bring it up. The inverse would be true if respiration and energy production is too high. It sacrifices nervous system function to accomplish this.
Why is copper high? Probably to fight off an infection. It will sacrifice ceruloplasmin and tissue integrity to get rid of the infection, so it sends copper throughout the body to kill the pathogen.
Serum potassium increases throughout pregnancy, peaking in the third trimester. Why? Because it's building a body, and the demand for potassium increases significantly throughout gestation, peaking when the fetus is at it's largest. So the mother releases intracellular potassium to be integrated into the fetus. Healthy high socioeconomic status women perform this function even better than poor stressed counterparts. Those poor stressed women can't sacrifice the extra potassium because the body is prioritizing host health vs. fetal health. The well off women can spare the potassium for the fetus though.
I think when we think about these things in the context of "what's the body trying to do?" and "maybe it's not actually making a mistake, and it's doing what it thinks is best?" the answer to many health problems becomes much more clear.
