Lilly Wachowski states in this video by the Netflix Film Club, at around 2:00:

And so we had the character of Switch, who was like, a character who would be, you know a man and blrgh, real world and then a woman in the Matrix, and, you know, that's both where our headpsaces were.

And a minute earlier (~0:58), about the studio blocking it, she says (in the context of the movie being about being trans in general):

I'm glad that it has gotten out that, um, that was original intention, but, the world wasn't quite ready yet [...] the corporate world wasn't ready for it...

Lilly Wachowski states in this video by the Netflix Film Club, at around 2:00:

And so we had the character of Switch, who was like, a character who would be, you know a man in the real world and then a woman in the Matrix, and, you know, that's both where our headspaces were.

And a minute earlier (~0:58), about the studio blocking it, she says (in the context of the movie being about being trans in general):

I'm glad that it has gotten out that, um, that was original intention, but, the world wasn't quite ready yet [...] the corporate world wasn't ready for it...