It seems obvious to me that people who go out of their way to purchase and consume nutritional yeast prefer to have naturally occurring B-vitamins over commonly available multivitamins. Why do most manufacturers “fortify” nutritional yeast with synthetic B vitamins? Many nutritionists believe the synthetic vitamins actually block the normal uptake of the naturally occurring ones, defeating the purpose.
In my experience, which is purely anecdotal, some of the largest consumers of nutritional yeast are vegans or other plant-based eaters. Some B-vitamins - most notably B12 - are predominantly or strictly naturally occurring in animal products. Hence, nutritional yeast is often fortified with B-vitamins because that’s what that consumer base wants.
I don’t specifically know the answer to your question about nutritional yeast but based on my prior experience working in the food industry it’s typical for the naturally occurring nutrients in food to have a shorter shelf life. By stripping the part of the food that goes rancid more quickly and replacing with something fortified it extends shelf life.