From what I’ve read, The Matrix wasn’t created as a trans allegory, it’s just that you can apply the fundamentals of its story to many concepts. One of the most popular interpretations happens to be gender identity because its creators transitioned years after the original trilogy ended.
I went back and looked at the articles I had read and dug a little deeper to get to an interview with Lilly Wachowski herself:
https://www.them.us/story/lilly-wachowski-mentoring-the-matrix-interview
To be honest, her statement doesn’t seem like either a denial or confirmation to me so 🤷♂️