1. Would animals already suffering from leaky gut syndrome still respond to Zn amino acid supplementation?
Yes. Absorption of amino acid pathway minerals is independent of leaky gut syndrome. Amino acid pathway minerals (especially Zn) have been shown to reduce levels of inflammatory cytokines. As inflammatory cytokines tend to target tight cell junctions, thereby aggravating the effect of leaky gut syndrome, reductions in levels of these compounds will likely have a beneficial effect, especially under stress conditions.
Modern genotypes of livestock have vastly improved performance expectations relative to a decade or more ago. In many cases feed intake is still restricted. Thus mineral source (in inorganic form) has become a limitation. Increasing dietary levels of inorganic source has limitations as the route of absorption becomes the restriction. By using the amino acid pathway route in parallel, more mineral is able to be taken up through the enterocytes. Simple stressors such as feed-restriction and lactation (vs. non lactating animals) increase inflammation which may negatively impact performance. Amino-acid pathway minerals have been shown to reduce inflammation.
3. With amino acid bound minerals being superior to inorganic minerals, disregarding cost would we ever do a total substitution?
If cost were disregarded, this could be a possibility, especially if reduced environmental excretion of specific trace minerals was important. However, practically speaking this would need to be looked at on a case by case basis.