They have neither confirmed or denied it being a trans allegory. It depends on how you interpret the response Lilly Wachowski gave in an interview a few years ago:
Continuing on The Matrix, you confirmed a couple years ago that it was a trans allegory —
No, I didn’t.
You didn’t? Tell me more.
Yeah, so that came from an interview I did for Disclosure. They had a bunch of Matrix questions. And the question they asked me was about Switch, who was originally written as a trans character who was male in the real world and female in the matrix. And they took that response and attached the question that everyone now references that it’s a trans allegory. And so it was slightly out of context, but I don’t sit here and put a stink up about it, because it is a trans allegory in that it was written by two closeted trans women. And so all of the things that are in it are super-duper trans. The idea of transformation, even the whole “My name is Neo, Mr. Anderson —” that idea of claiming identity, it’s undeniable.
They have neither confirmed or denied it being a trans allegory. It depends on how you interpret the response Lilly Wachowski gave in an interview a few years ago:
https://www.them.us/story/lilly-wachowski-mentoring-the-matrix-interview
So it was an unintentional trans allegory?
Closeted people often express their desires subconsciously. Well, frankly, most people do.