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 Matrixquestions. 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