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.
https://www.them.us/story/lilly-wachowski-mentoring-the-matrix-interview
Artists often subconsciously put their own ideas and beliefs into their art, as art is a reflection of the artist to some degree. For example, I really like the color blue so I tend to incorporate a lot of blues in my designs. This doesn’t mean I’m sad, or that I’m tying to evoke the feeling of water, it just means that I like blue so I tend to begin with the blue color and consequently my designs lean towards blue pallets.
very similar to the game Celeste which was made by a questioning/closeted trans person, so the whole game pretty much follows the trans experience. The creator actually confirmed canonically that the character (Madeline) is trans too.
“During Celeste’s development, I did not know that Madeline or myself were trans. During the Farewell DLC’s development, I began to form a hunch. Post-development, I now know that we both are.”
AAGH MY HEART 😭😭
A quite intentional trans allegory that also stands as exploring a lot of parallel concepts, and since transness is not popular, its better not to admit it and let trans-panic scare away Matrix fans who couldn’t handle it.
The Matrix analogy works better for me compared to my ASD experiences than my midlife enby status.
No, it has a recurring theme of transformation. You could read the first part as a trans allegory, but you could squint and do the same for Star wars or Harry Potter. It’s the story of the chosen one
Not everything written by a trans person is a trans allegory. Trans people can tell other stories…a trans allegory is about that specific personal journey, not just influenced by it