That quote is talking about the first movie. The original one. Neo’s story is a cleverly hidden but also extremely thin metaphor about a trans woman finding herself. That scene with the red and blue pills is literally Neo choosing estrogen over antidepressants. “Mr. Anderson” with that iconic over the top emphasis on the mister is Neo getting deadnamed. Neo has this feeling that the world is wrong (gender dysphoria) and finds the truth in online chat rooms and in a bar full of people who wear full leather outfits (a crude stand-in for the LGBT community).
I could keep doing this for every part of the movie but you get the picture. And it’s all canon.
I know but this article is from 7 August 2020 so I got the impression, given the climate of the day, for this Matrix to be even more about it.
There are movies built around a social issue like Philedelphia or Leaving Las Vegas, but I think the filmmaker needs to use gritty realism. Trying to steer The Matrix Science Fiction movies in that direction about trans I thought would probably be a disaster.
I could keep doing this for every part of the movie but you get the picture. And it’s all canon.