Perversely, these monopolies are often granted on the basis of 'natural monopoly theory'. If it's a natural monopoly, why does it need to be further enforced (preserved?) by a law?

Eh, what? What monopolies are granted by law on the basis of natural monopoly theory? As you state, there is no reason to put them into law; natural monopolies are usually the ones who are broken up by regulators, to enforce competition (e.g. telecoms, energy manufacturing/distribution, public transport, ...)

These same monopolies you're mentioning (were|are) in fact legally protected from competition.