This is, I think, the same reason why we should be sceptical of genetically modified foods - not because the process is unnatural, or is inherently damaging - but for a more banal reason, because it is similar to eating foods with a lot of additives. In both cases you fundamentally lose control over the building blocks of your diet. If you can only choose between different highly processed foods, that means you need advanced domain knowledge to be able to make a reasonable judgment about the trans-fats, the MSG, or the highly processed sugar. But, at present, these additives are not mixed into the ingredients, you do at least have the option of opting out.