Yeah, it sounds to me like she has issue with just that specific thing being treated as a trans allegory rather than the whole thing, the film, The Matrix, itself, as trans allegory as a whole, and the idea that it was purposeful rather than happenstance.
It sounds more like “we were closeted at the time, and we unconsciously were putting in trans allegories to our own paths and ideas” which still means its trans allegory, even if it was unintentional at the time, because they still hadn’t “come out” to even themselves yet.
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.
In other words, it’s undeniably trans allegory, but perhaps that wasn’t consciously on their mind at the time they wrote it.
Thanks for the link, I hadn’t read that one. Definitely clears it up a little.