Cody, I think that there is potentially a whole lot to that.
I do not know if there are different forms of gluten, and a proper sourdough fermentation process generally does make bread better for you for many of the reasons you mentioned.
I know that people who are severely gluten-intolerant generally have issues with all forms of gluten, and I do not know of any studies, whether RCT or just surveys, that have looked into whether there is a differential effect from heirloom sources.
On a very personal level, I do believe that there is something to the idea that all of our "New, improved" crops have exposed us to dietary proteins, and other compounds, that our bodies have never seen before in known history, as well as abnormal levels of chemicals like gluten that are causing us a wide variety of issues.
I also believe that there is a lot to the idea of historical exposure of ones direct ancestors to certain nutrients and food sources can influence how well you personally tolerate said food sources.
This is a very new area of nutritional science, and one that I think is going to develop quite a lot during our lifetimes and beyond.
I, too, believe that the older methods of food preparation and non-genetically modified or hybridized food sources are, together, our best shot at ideal health from nutrition.