I'm not discussing taste or health. I'm saying that your atomic characterization of both systems being the same is in error.
While a molecule is certainly a molecule, it's all about how the plant got the molecule. If it was provided naturally by microbial action, then you've included the microbes in the deal and you get all the benefits associated with this relationship. Increased immune response, resistance to insect predation, full nutritional interaction, etc.
When the molecule is provided by a bottle-fed routine, you have removed the role of the microbe, and you've removed their benefits as well.