An interesting article.
Personally, I haven't changed my mind about the film itself. I don't care for it, and outlined why in my review (see link below). It picks up on many of the aspects you describe here.
I'm fully aware of the transgender thing, but I would say that even if that's what it is intended to be about, once a film (or book, play, piece of music, or any piece of art) is out there, it is up to the audience to decide how to interpret it. That is out of the artist's hands, regardless of their intent. If that interpretation isn't picked up on, it begs the question: Did the artist fail? I certainly didn't think it had anything to do with transgender issues when I saw the film at the cinema in 1999, but I definitely saw Christian allegories. I think background, personality, temperament, religious beliefs, and so forth affect everyone's way of looking at art. Two people can look at the same piece of art and come away with two radically different opinions. Unfortunately, we have to accept that includes the nasty right-wing types you refer to here.
One thing you have made me rethink: Perhaps Lana really did deliberately stick two fingers up to the audience. But I don't buy into this shocking-audiences-out-of-their-apathy argument for a film of this kind. Yes, I agree there are far too many damn reboots, sequels, and an interminable amount of superhero films. Yes, I wish mainstream Hollywood would snap out of its creative inertia when it comes to lazy reliance on old stories and take some proper risks again.
But because outside mainstream Hollywood, cinema remains as innovative, incisive, challenging, and vibrant as ever (think European cinema, Korean cinema, Japanese cinema, British film, and even the US indie scene), I struggle to give a damn if Lana has me in her crosshairs. Lash out at the audience all you like, Lana. (With no offence intended to you of course, Cole, as I know you are an honourable writer in mainstream Hollywood with proper integrity, and I have much respect for you). :)
Anyway, here's my original review (I expected it to be a hit and it wasn't - that at least I got wrong):
https://medium.com/simon-dillon-cinema/film-review-the-matrix-resurrections-d61cbb07707f