This is a valid point. And it is a valid (and very important) question, for a scientist. However, there is an obvious answer that needs a ton of investigation. The "container" of a vitamin C pill vs a citrus fruit (or any vitamin C rich vegetable) vastly different. And in both cases, they are interacting with a system that has a mind-numbing number of variables, most of which are only poorly understood if even accounted for at all.

But ignoring all those microbiome + immune/endocrine system + (human) cellular metabolism variables, I pose this question in response:

The ammonium nitrate in human urine and TNT explosives is chemically the same. Why would it have any different effect regardless of the form?