Renaissance I and II can’t possibly portray the actual history. I think Ushgarak made that point earlier: They both start by elaborately pulling us into the Zion database archive. We now know that Zion is destroyed at the end of each loop of the Matrix, the One is allowed to chose 23 hapless oblivious humans from the system to be unplugged and together they rebuild the city.
Of course such database stories MUST be there, as every free human is supposed to at least believe that a man was born in the matrix, broke free (or was freed by rebels), and freed the first minds.
I see both short-stories as another stroke of Wachoski Brother genius. The humans are the bad, evil, aggressive, intolerant (insert other synonyms here please) species, that attack and harass the nice, friendly robots and AIs who only after being attacked strike back, and are almost forced, by us, the humans, to use us as a power-source.
As agent Smith says in M1 we wouldn’t accept the perfect world of bliss and happiness, we seem to thrive on misery and pain. Of course we would accept such a horrid story of how mankind fell. Right?