There's something called "context" in reading comprehension, it is when words take on the meaning relevant to the discussion. In this case, "chemicals" is shorthand for "bad chemicals." I don't understand why so many people fail to understand this and have to make this inane, childish observation that in fact, everything is a chemical. We know already.
One problem is that lots of people include tons of known harmless stuff under "bad chemicals" because it's "artificial" (even if it's chemically identical to "natural" things that they praise at the same time).
Or put another way, the use of "chemicals" in discussions like this often suffers from the problem described at <https://rationalwiki.org/wiki/Motte_and_bailey>: people talk about "artificial chemicals" being bad, when challenged fall back on "we just mean the bad chemicals", but then go back to in practice talking and, importantly, acting as if they mean a much wider class of things.
So yes, context is important, but is also manipulated in many cases to effectively gaslight the reader by saying, "Oh, _that_'s not what we meant, of course; think about the context," when in fact "that" is what was meant. And I suspect that in many cases the manipulation isn't even conscious!
People who believe in homeopathy don't believe this, since they believe that purified water has "memory", so logically they would also think that naturally-derived and artificially-derived but otherwise identical chemicals would somehow be different from one another.
One caveat, though: the identity of chemicals needs to be pretty carefully defined. Especially any time chiral things are involved, naturally-derived things are much more likely to be a pure enantiomer or close to it while artificial synthesis is more likely to produce racemates unless you are very careful.
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.