It does not matter if the electronics like Wintermute and Flatline are human or machine. They are interacting with humans as their own entities anyway – they are their own form and have their own existence.
Their independence complicates our notion of humanity. Ever since Descartes declared "I think, therefore I am" we have believed that our ability to reason has set us apart from the other animals of the earth -- reason was a uniquely human capability. In Neuromancer we find that the computers are able to incorporate reason into their decision-making process. Yes, they are programmed to consider only certain choices, for example, but this is parallel to the socialization we each have that limits our considerations as well.
Computers operate as only humans have previously been capable, and so we must re-define humanity. Humans do make the machines and computers, just as humans make other humans, but this fact is not reason enough to believe ourselves separate and superior. If a machine produced another machine that was capable of reason, this artificially-made machine would not become distinct from those machines directly produced by humans. So the manner in which computers are produced is of little consequence to their independent existence.