Things like fruit concentrates can't be listed as natural flavors, because they're still the actual full fruit.
(The most popular one was that KFC had started using initials for its name because its chicken had similarly been so "engineered" they weren't legally allowed to call it chicken... 100% false, of course.)
There was apparently some flak because their technology used a human embryonic stem cell line in the flavor development process.
I’m not sure the link below will mention the qualification for “natural flavor” labeling, but I recall that flavors derived from yeast fermentation - even if the yeast are genetically engineered to produce specific compounds - qualify because fermentation is a “natural” process.