In M3, we see the world through Neo's "blindfolded" eyes as a kind of virtual reality consisting of glowing yellow representations of machines and their structures. The vast majority of those who see M3 for the first time feel frustrated at this point, because it feels as if we are being asked to believe that Neo can see better without his eyes by some miracle of God. But there is no miracle here.
Going all the way back to M1, we see that Neo can "feel" the machines. He says it in the phone booth at the end of M1, he says he can feel them even more directly in M2, and of course the Oracle tells us in M3 that Neo derives his power from the Source. One of the senses Neo is surely "feeling" is the reception of projected machine images from the Source. Neo sees machines the same way sentinels and other machines see each other. Think of it as if all machines were wearing wireless virtual reality goggles that change or enhance what they see in the real world. Merely wearing those goggles is not enough; obviously, there has to be something broadcasting a signal to the goggles for them to be able to display anything. When Neo entered the Source, his connection to the Source was "enabled," enhancing his senses of machines in the real world. This enhanced sense is why (right after exiting the Source) he could sense the sentinels' intent to launch the sentinel bomb before it was launched, and why he was prompted to turn around and "attack" the sentinels as they chased after the Nebuchadnezzar crew. The connection to the Source enables every machine connected to the Source to see other machines.
Why did going blind make Neo see better? Most likely, Neo's normal eyesight was actually getting in the way of fully experiencing his new connection to the machine world (his "virtual reality goggles") through the Source, perhaps because his brain didn't know how to process multiple spacial awareness senses at once.
Sentinels and other machines have special lenses allowing them to see more than just each other. In "Matriculated" (The Animatrix), the "runner" machine can see a human running even when the human goes behind a hill, because the machine has extra sensory devices devoted to perceiving the surrounding environment. However, Neo doesn't seem to have such vision devices, and his vision also has other limits. Neo couldn't see his own ship or Trinity, so Neo was still visually "impaired."
Notice that when Neo sees Bane after being blinded, he doesn't see Bane - instead, he sees a slightly inaccurate flaming version of Smith! When machines broadcast their real world positions to the Source, they aren't just sending (x,y,z) location coordinates. They are sending the same thing that is communicated and utilized within the Matrix: RSI (see Introduction: People, Places & Things for a definition of RSI). Smith cannot project his RSI into the actual real world because there is no "Matrix within a Matrix" (Trinity still sees Bane). But Smith's RSI is still being projected back to the Source, which Neo is connected to. Therefore, Neo is receiving the rough RSI image of Bane-Smith from the Source.
Everything Neo sees in the real world consists of some kind of beautiful gold-colored entity. Everything except Bane-Smith. Why does Neo see Bane-Smith as a flaming Smith instead of some kind of gold-colored image that looks like a machine?
When the Source broadcasts RSI images in the real world, it makes sense that it would broadcast various types of entities with a different look, the same way a GPS system might broadcast blue dots, red dots, yellow dots, etc. to represent different types of cars, planes, etc. The system is able to spot exiles readily and quickly while inside the Matrix, so my guess is that exiles are spotted just as easily outside the Matrix (so the flames represent Smith's exile status). But consider that Smith's exile status is not the only thing that makes Bane-Smith different. There are actually three qualities that set Bane-Smith apart from other entities Neo sees in the real world:
What a unique entity Bane-Smith is! One sentinel would probably say to another sentinel, "Look at the human exile virus - you don't see one of those every day." Each of the above differences (human, exile, virus) may actually have contributed its own unique visual effect to the the overall look of Bane-Smith's RSI.
When we are given a machine view of Neo (i.e. when he's reviving Trinity), both he and Trinity appear in green code. If machines jacked into the Matrix are given special coloring, why aren't humans given special coloring, especially redpill hackers like Trinity or Neo? This question is especially interesting considering that when we see Neo reviving Trinity, he had just exited the Source and established a connection with it, making him even more unique than before. If that doesn't produce special coloring within the Matrix, what would?
First, to address normal humans in the Matrix (bluepills), they all appear in green code, just like cats and buildings and anything else that is part of the core of the Matrix simulation. The billions of humans that form the Matrix are providing hardware (processing power, RAM, and hard drive space), they are running the software (core programming) of the Matrix, and each of the bluepill humans themselves are a part of the core of the Matrix simulation. By stark contrast, a firewall is not part of the core simulation – it is its own hardware outside of the system, which is why Seraph appears gold. A firewall has to be separate from the core programming of the system, or it would be too easily compromised.
As for hackers, hackers who jack into the Matrix would need to appear in green code so that they’re not so easily and immediately identified as hackers in the system. A hacker probably wouldn't attempt to enter the Matrix in the first place if they didn't first figure out a way to make themselves appear in green code (i.e. "part of the Matrix simulation").
And as for Neo, Entering the Source gives Neo additional power within (and outside of) the Matrix, but the function of The One would be greatly compromised if the system flagged The One some other color within the system. Neo would have a very hard time freeing minds if he's always having to run from agents.
How does Bane-Smith project his image back to the Source if Bane is just a normal human (not a special human like Neo)? The only reasonable answer is to say it is the headplug that every Matrix-grown human has. The Smith program knows how to utilize this headplug while conciously awake (as does Neo subconsciously since he is the One). Normal humans, when awake in the real world, apparently have inactive headplugs since Neo cannot see Trinity in the real world after he is blinded (Trinity's headplug was inactive).
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