Carnists claim that humans are justified in eating meat because it is their natural place within ecology to do so.
The concept of a food chain is an invention that helps give an introduction to concepts in basic ecology. It is too simplified to even be useful in any serious context, such as in cases where two species (usually one being invasive) predate on each other (or on each other's young), for instance, or when species eat their own young. There is no "food chain" in that context in any meaningful sense, it's just a simplified model for teaching basic biology to school children.
Even if the food chain actually existed as a real thing, is drinking other species' milk really apex-predator behavior? Or putting a stack of neatly extruded pepperoni into a shopping cart? So, some imagined "food chain" isn't actually why carnists do what they do, and isn't their real justification.
Even if you accept the argument that humans are part of some imagined natural ecology that somehow includes hotdogs, it does not follow that what is natural within ecology is automatically ethically justified. Is eating the young of your own species OK because animals do it in the wild?
Even if one somehow ignores all these problems, meat is still an ecological disaster that also starves people in third-world countries, which serves to only destroy the very "food chain" being argued for. So one can't really use that as justification for eating meat or consuming animal products.