The writers wanted to have a character in the movie who appeared male in the matrix and then female in the real world, but at that time they were told to change that. They have said that yes, the movie was intended as trans allegory though, and I would imagine as the creators they would have the final word on that.

The writers/directors were both trans and the baddies keep dead-naming him and trying to drag him back to his previous dull existence that he hated. If he became a woman it wouldn’t be an allegory it would be a literal trans story

During the opening scene, Cypher and Trinity are discussing Neo while computer code is being typed out on screen. The word “trans” is the second word to appear in the code, at the 43 sec mark of that video

Conversely, the closing scene features the words “System Failure,” where the camera zooms in between the two words before zeroing in on just the two letters M and F, at the 3:18 mark here

Neo’s dead name, Mister Anderson, is extremely male coded. Andr- is the Greek root for man, the honorific Mister, and suffix -son. Neo by contrast is very gender neutral

The estrogen pill they gave trans women in the 90’s, Premarin, was a red pill. There’s a scene where Morpheus tells Neo “Hey, I know that everything about your existence feels wrong. You don’t know what it is, but it’s always there like a splinter in your mind. It’s everything you feel, taste, and touch. You know exactly what I’m talking about, right?” He then offers Neo a red pill. Neo takes it and then it immediately cuts to a visceral, graphic, and literal rebirth scene.

There’s lots of stuff in there that’s trans coded if you’re looking for it