I would alternatively say: "However, an implied assumption, is that the global polypeptide conformation is necessary for function and/or its control".

The concept of having the apo conformation being the one associated with function is already accepted as wrong in most cases, mostly because it implies that the protein is a frozen lock, waiting for a key to operate on it (the lock and key old model).

I think it is nowadays widely accepted that the function-associated conformation is either reached or stabilized only in response of the apo conformation to a substrate binding event.

This is not something new. It all goes back to the two modes of response to substrate binding.

In an induced fit scenario, in order to reach the conformation at which "function" (i.e. chemistry) starts a substrate has to bind a specific site in the apo conformation of the protein and this, in turn, will induce the conformation change from the apo conformation to the conformation from which function starts.

In a selected fit, the substrate-free protein fluctuate between a conformation different than that from which function starts and a conformation from which function starts and a substrate then binds only to the function-associated conformation and by that, stabilizes it.

The Equilibrium shift mode is sort of a hybrid between indiced a selected fit, whereby the conformational changes pre-exist in the substrate-free protein and the function-associated conformation is stabilized after substrate binding to either one of the conformations.

In regards to the relation of the apo conformation to the product of protein folding, consider what would have happened if the end-product of the protein folding process of an enzyme would have been directly its function-associated conformation - you would have had no structural means for control over that function.

If you look at the native conformation as being found at the lowest free energy tip of an energy funnel, then both the substrate-free and function-associated conformations share that minimum. I'd much rather think of the substrate as shifting that free energy funnel into exploring other conformations.

I understood your question and I think the term "conformation" and "native" in protein science is sometimes not well understood. 

"native" related to the protein folding aspect.

"conformation" is comprised out of an ensemble of structures, not one unique structure that are accessible within the same free energy well, separated from other free energy wells by more than kT. Now, this includes the entire protein structure including intra- and inter-domain structures.

I related to the "function" part of your question in regards to the "nativity" of the structure in the terminological context given here.