The safety factor is the main point!
The vast majority of the chemicals in food are untested (and a great many are bioactive). Which is alarming. Rather than allow any chemical which is not known to be harmful, why not switch to allowing only chemicals which are known NOT to be harmful? Oh yeahhh... that would hurt profit margins.
The food industry doesn't give a F about producing safe food, they care about money. This is evidenced by the preponderance of hydrogenated oils, preservatives, artificial colors, enriched flours (which might as well be pure sugar), artificial sweeteners, high-fructose corn syrup (which only exists as a product due to wasteful corn subsidies), etc...
I haven't seen the movie, but I'm struck by the remembrance of an NPR interview I heard with the guy behind Food, Inc.
He related a story about the extremely high levels of E. Coli in our dairy herds, how it results in infections and deaths in those that eat it, and how it is caused by the diet they were feeding the cows. Research showed that by intermittently feeding them grass, the E. Coli levels would be drastically reduced. Instead, the food industry began researching other means of killing the E. Coli, and were considering adding ammonia to the cow's feed.
Why introduce another complicating factor when you could just use the safe, natural solution (grass)? Would it hurt their profit margin that badly?