Because when people talk about "chemicals", they are often flirting with the appeal-to-nature fallacy (https://en.wikipedia.org/wiki/Appeal_to_nature).
While "better because natural" isn't some infallible nutritional law, it serves as a very solid rule of thumb for those of us who don't have the time or motivation to more thoroughly study the science behind it.
Tribes completely isolated from modern society have been proven to have extremely rich knowledge of the plants in their environments. As humans, we are extremely familiar with plants found in nature.
GMO foods are chemically speaking much closer to natural than this veggie patty we are talking about. It lies on a spectrum so arguing about how neatly something fits a definition is missing the point.