Honestly, the definition of natural is a huge problem.
I don't think that most people use natural in the same way that Whole Earth means it. However, when you try to define what most people mean, you run in to some huge problems.
natural: Present in or produced by nature
nature: The world of living things and the outdoors
In other words, using these definitions, humans would be part of nature (we are living things), and anything we do would therefore be natural.
I will assert that most people (other than perhaps some philosophers) would say that a steel building is unnatural, but loganberries or sea salt would be natural.
With that said, my definition for natural could be:
natural: anything found without modification in nature, or those things modified using processes found in nature.
In this way, hybrid plants are natural, because they are "modified" by selective breeding. And breeding is a process found in nature. However, an argument could be made that grafting is not found in nature, and therefore plant material from grafted plants is
not natural, even though the two "halves" are themselves natural.
Wine wouldn't necessarily be natural, because it isn't found in nature (pressing and distilling are not natural processes to the best of my knowledge), but wine definitely contains natural ingredients (unless grafted; see above).
The real issue comes up when you're discussing GMOs. Technically, a GMO is just a "graft" at the genetic level: naturally occurring genes are spliced into the gene sequence of the primary plant to create more desirable characteristics. And, believe it or not, this process is actually found in nature: horizontal gene transfer. Obviously, modern genetic modification is highly guided by humans, and performed in settings that I would bet are widely considered unnatural, but nevertheless, the core process is a natural one.
Now, what about another "unnatural" material: glass. Glass is actually found fairly commonly in nature. Volcanoes spew glass material. And much of the sand on the beach is glass. While we have fairly complicated processes today for creating high quality glass, at its core, glass is just a natural material (silica) that is heated to a high temperature and then cooled, a process which can widely be found in nature.
I relate the problems of defining nature to the same problems that the word chemical faces. There is a clear, scientific definition of the word chemical, but laypeople have a different definition. Chemical is used to describe "bad" chemicals. While "good" chemicals get different names, like scents and flavors.
In the end, natural means exactly what you mean it to mean.