Unfortunately I think only the Wachowski's can clearly answer that. They wrote the story and it all comes from their imagination. In all reality, everything else posed by us is simply guess work and speculation. I discovered this page while exploring an answer to your question. The second theory seems more plausible theory in my mind.
Submitted by Chris Dorst
First-off, I'm not sure if I believe this theory or not myself, but I thought it was interesting nonetheless. This theory attempts to explain Neo's ability to see the world in gold light after he becomes blind in Revolutions.
Throughout the trilogy, Neo gains more and more abilities. This is not only apparent in the Matrix, but in the real world as well. In the Matrix, Neo flies, stops bullets, and is faster and stronger than everyone else (except Smith). He can do all of these things because he is the One, the "result of the remainder of an unbalanced equation inherent to the programming of the Matrix; the eventuality of an anomaly." Outside of the Matrix, Neo destroys sentinals and can see the world in gold light. The Oracle explains his ability to destroy sentinals by telling him that his power extends back all the way to the Source (the machine mainframe), and that he manifested that power to destroy the sentinals. After Neo becomes blind, he can see the supposed real world in gold light. This ability is never completely explained in the trilogy, which is why there are many theories that try to explain it.
My theory: The gold light that Neo can see in the real world is actually the code of another Matrix, or level of the Matrix. Thus, the world where Zion exists is really part of a Matrix, or a "Real World Matrix."
Gold Code II
Submitted by Rewris
The "Gold Code" is in my opinion is simply the energy force of the machines in 01 (Machine City). That's all it is, the catch about it, the thing to bake your noodle, is why Neo can see it. But then again, I think the answer is quite obvious: Neo is the One. I have read some theories on the One, but I can't agree with them for the simple reason of them denying Neo of the power that everything in the movie conveys him to have or be about. Neo is the One; he can modify the Matrix as he sees fit, to some extent yes, of course he is limited. He can stop bullets in midair but he can't manifest them in out of air. The Matrix is based on rules, it is a simulation of real life, made to be that way so the humans would embrace it and not wake up. So that it will seem all the more "real" and less dream-like. Although a lot of big things may happen, like a man flying on the freeway, it is still small on a certain level.
There you have it, Two theories on why Neo was able to see the "Gold" code. I hope I've helped at least a bit.