I had to look this up because I wasn't aware of it. It seems the creators themselves have refuted this and said that it was a journalist twisting their answers.
https://www.them.us/story/lilly-wachowski-work-in-progress-s...
https://www.them.us/story/lilly-wachowski-work-in-progress-s...
'It's not something that I want to come out and rebut. Like, yes, it's a trans allegory — it was made by two closeted trans women, how can it not be?! But the way that they put that question in front of my answer, it seems like I’m coming out emphatically saying, “Oh yeah, we were thinking about it the whole time.”'