One thing many people dont realize is that endotoxin is not simply just "produced" by bacteria, it is the result of the bacteria dying, it is a cell wall component of the bacteria
This can be released when it is killed by an antimicrobial, or when the immune system/another bacteria kills it
A thriving overgrowth that isnt dying off does not necessarily produce endotoxin, but when the immune system is constantly fighting it, but it is not getting killed off, this is when problems occur, especially when the gut is leaky/damaged/not immediately dealing with the endotoxin
If your gut is leaky, and you have specific bacterial overgrowth in your small intestine, and you take berberine, it could generally just cause a spike in endotoxin, but not be enough to fully kill off the overgrowth, so if you keep eating carbs (whether fermentable fibers or even sugars/starches depending) in this scenario you are just giving yourself mild endotoxemia
One of the many reasons it's important to have a goal with your compound use and account for surrounding variables