There were not any aliens in the Matrix, not even in back plot.
Actually, I think that it's more likely they just didn't bother to dodge punches, as punches are inherently non-lethal. As was seen in the films, the agents could withstand brutal physical assaults that would have dropped anyone else with broken arms, ribs, you name it. Bullets, however, ripped through the body they "inhabit", and kill it, thus necessitating a dodge.
The robots were created by humans, through the use of Artificial Intelligence, and while we are never given a direct point on who started the man/machine war, we are told directly that humans scorched the sky, creating a thick albedo that kept out the sun, depriving the solar powered robots of their power source. Apparently, though the robots anticipated it, and figured out a way to jack humans like D cell batteries.
However, humans could still get out were they conscious of what was going on, and permanent sedation wasn't really practical, and would lead to reduced capacity, so they came up with a way of "tricking" the brain with computer codes, allowing the humans to exist in a virtual world that would conform to what their minds expected there to be.
The first attempt at this was disastrous, the "perfect world" scenario being one that humans innately recognized as wrong, and so many humans began to wake up. Then there was the first "One", who could manipulate the code, a weakness in the program that simply could not be written out, and so the machines were forced to adapt the rules, since a perfect order simply couldn't work. They thus allowed Zion to exist, with a certain number of humans, both born there, and "freed" from the Matrix. This kept the world from breaking down, and just required a purge of the free humans every so often when another "One" would appear, and begin the cycle again, until Neo breaks it.
The entire thesis point of the OP is actually riddled with inconsistencies. When a man is having a stroke, and smells burnt toast, is that because there is burnt toast in the room? Or how about hallucinations, where the brain creates auditory, visual, and even tactile illusion all on its own? the brain controls everything in the entirety of our body, including of ability to touch. It regulates our response even to atmospheric pressure.
As to the issue of subjective vs. objective reality, we have role-playing games now, where we created a single static reality that each person acts in individually, conforming to the set laws of the virtual world. A night elf in World of Warcraft doesn't suddenly become naked cause your troll had an errant thought. Yes, each person has a degree of individual will, they can choose things, but those choices are limited by the physics of the virtual world, much like in World of Warcraft. Simply look at Neo as being the asshole who finds a GM mod for his character, and cracks out his avatar to near godhood.
The "Lady in Red" was not code for Illuminati, but a distraction built by a... shall we shall slightly "oversexed" geek boy. She was used in a training program in order to facilitate a lack of attention from Neo, which succeeded as it was supposed to. The training part was to get Neo to understand the true ramifications of the virtual world of the Matrix in a safe environment.