I’ve been struggling with how best to express it, but I think it comes down to the recapitulation, in the musical sense, i.e., how a composer will revisit a theme and take it in a new or at least different direction; to the möbius strip/meta quality; and to the banality of the evil of the antagonist: why, yes, that’s exactly how I would expect a deranged and resentful program to punish its (perceived) enemy.
The continuing question of perception, both of reality and of values, is a key element of all of that.
It’s true to the original, repeating parts of it without ever being the same. The River of The Matrix, or the Matrix of Thaddeus, if you will.