First off, glyphosate tolerance has nothing to do with BT (or any other bacteria) — that's a completely different genetic modification that's associated with a specific herbicide tolerance. The addition of BT traits specifically allows/empowers the corn plant to generate enzymes equivalent to those produced by B. thuringiensis bacteria (which are toxic to certain species of worms that feed on corn).
Using a specific bacterium as a biological drug, in order to provide a food product with the ability to modify the body's immune system response, is basically the same concept, except that it's disguised as a "probiotic", so it slips in under your radar.
How do you think that product will magically prevent all those autoimmune diseases? In order to have a global effect, it will have to perform similarly to helminth therapy. IOW, my guess is that it will promote an alternative immune system reaction against the particular bacterial pathogen that they have selected to use. The immune system response that it promotes will have to be dominant, in order to distract the immune system from the other reactions that it is designed to preempt. That infers that it will have to generate an alternative inflammatory response that the immune system perceives as more of a threat than the antigens that it is currently reacting to (with various concurrent autoimmune issues).
Is an inflammation source that the immune system perceives as a greater threat than any other current inflammatory event likely to be a safe choice for long-term health?
Maybe — maybe not. Are individuals who have a lifetime infection with helminths (so that IBDs and other autoimmune-type issues are prevented) noted for their longevity?
That said, I will concede that such a product may well be safer to use for treating/preventing autoimmune-type issues than the many drugs that are currently being prescribed to alter the body's immune system response, because those surely diminish average longevity, also. The safest approach would be to research new and innovative ways to use diet to control so-called autoimmune diseases, because virtually all of the common autoimmune-type issues appear to be caused by external antigens, in conjunction with a weakened or otherwise compromised immune system (usually associated with a vitamin D deficiency), not by an overactive immune system. And therapies of the type proposed are usually designed to downregulate what the researchers incorrectly perceive as an overactive immune system.
Note that the claims behind this concept validate my long-time claim that all so-called autoimmune diseases have a common origin. If they didn't have a common origin, then no single product could be used to treat them all. The problem is that the medical community is still trying to promote the use of drugs, when the cause of the problem is dietary. It's the same old mantra — treat the symptoms, not the cause. But doctors don't want to be dietitians — they want to write drug prescriptions. Why? Because they have a monopoly on the ability to write drug prescriptions, and that guarantees them job security in the long run. By contrast, they don't have a monopoly on anything related to diet recommendations, so they're not even interested in learning more about it.
I don't have a problem with using drugs to help control symptoms of disease, but I do have a problem with drugs being used as the exclusive treatment. The primary treatment should be based on dietary changes, not on drugs.
Tex