Idk if The Matrix was originally intended to be a tranny allegory (obviously the Wachowskis would've denied this in 1999 if anybody asked, but it was a more innocent time so nobody did). In retrospect it is a window into the unhealthy obsessions of the type of nerds who are at risk of hideously trooning out in middle age:
* The PVC/leather aesthetic probably came from the Wachowskis' porn viewing habits - we now know that long term porn addiction is common/ubiquitous among AGPs
* Carrie Anne Moss plays a (moderately ugly) Dommy Mommy - the nerd fantasy about butt-kicking babes taking charge of the situation (and his penis) is rooted in his own passivity and failure to develop a normal masculine personality.
* The bland, Aspergerish emotional flatness of pretty much every character who isn't Elrond or that turncoat guy
* On the internet, nobody knows you're a dork who writes code in a cubicle, and you can have a l33t hacker name and cool shades and everything. Neo is a Mary Sue for socially maladapted Special Boys who dream of unearned power and prestige, and doesn't really develop as a character so much as put on a new outfit and download new skills. Which isn't really that far from the kind of dress up/identity games that end up with nerds convincing themselves they're a dragonkin or a cute uwu girl or whatever
* Neo is also completely atomized and alienated from society at the start of the movie. He has an unfulfilling job that he hates, but there's no indication of parents, siblings, a girlfriend or normal social relationships of any kind in his life. Until he hooks up with his cool internet friends who encourage him to be his "true" self
* The high concept of The Matrix itself foreshadows our current technologically mediated pseudosocial dystopia where what previous generations and Ron Burgundy might have called "making love" has been, for a lot of people, replaced by sterile internet masturbation or equally sterile, mechanistic fucking
The Matrix is a kind of clammy, off-putting, slightly feverish place like a visual representation of a nerd's limp, sweaty handshake. I'm not saying everybody who goes to see THE MATRIX 4: BILL AND TED'S BOGUS NEOVAGINA should be put on some kind of watch list in case they start tucking their dick and dancing in front of a mirror. But maybe they should.