At a fundamental level, this is all about derivatives. 

Nominally holding commodity A, while it is stored as commodity B, means you hold B and you also hold a derivative that is short B and long A.  And your unit of B that you are holding should be in escrow in case the derivative goes sour.

If the derivative short B and long A is inextricably tied to a unit of commodity B, then it is safe from default, but there is not much advantage compared to just trading commodity A.  If they are severed, then there is risk of default, and the risk is tied to whoever is the counterparty to the derivative, which means they are not fungible.

It is premature to speak of how a block chain or somesuch could implement deriatives trading, before the inherent issues are resolved conceptually.