Forget the "Zion is a Matrix" theory. The truth is worse. After centuries in the pods, human consciousness IS machine code.
I see a lot of people claiming nobody ever left the Matrix and that Zion was just part of the simulation. But then why does Trinity see the sun after breaking the clouds? There would be no point in simulating sunny weather and clear skies with a star above the hellish digital world. It would be more and more clouds until they descend again.
To play devils avocado though, Agent Smith did indeed transfer from the Matrix to a human, which proved several things. First being that a human brain can support AI as a standalone system, and second, that human life and digital life is transferable and therefore indistinguishable.
The real conclusion I came up with is that humans growing up in simulation from birth to death, for possibly hundreds of years, means that any consciousness that escaped the Matrix going into Zion would be machine code from birth as well. Because the machine cultivated the humans and raised them as well as recycled them. At this point in the Matrix, my strong belief is that everyone is machine sentience.