Penicillin the substance existed in nature, penicillin the medicine is a human invention. Is stretching to call it natural. It's like calling high-fructose corn syrup natural. It comes from nature, but it's hardly naturally occurring.
I don't see how - the whole of the world's early mass production was simply naturally growing the mould in tanks. That was a huge part of the challenge of producing enough volume, and how to accelerate that fermentation and extraction. It was very much a natural product that was effectively farmed, and not much different to producing beer.
That we have now found chemical means of production, and identified active ingredients doesn't change that history. You might not legally be able to label penicillin or opiates as a natural remedy any more, but in prescription medicine the production method is rarely or never labelled.