While I can understand the Wachowski sisters wanting to spin the Matrix as a trans allegory, and there are many parts of the movie which that have a parallel to that narrative, it is my opinion that it is an apocalyptic, Abrahamic, dystopian allegory. There are so many references to biblical scripture and mythological archetypes that it seems a bit too intellectually lazy to just say it's about being trans. It seems a little convenient that the Wachowskis claim this as soon as they get triggered by conservative groups linking the red pilling of people to leaving the democratic liberal hivemind. I'm not denying that if you try really hard you can make an argument for it being a trans allegory, but it takes some real mental gymnastics to get there. I mean... let be honest here... Neo's life ends with a cross of light pouring out from his body....
The Matrix, to me, will always be a movie about the downfall of man to AI or the false Messiah, and the savior coming to wipe clean the sins of man and save them from destruction.