It won't bring in the same money, don't put your weird tranny shit
Now :
This is marketable in certain demographics, but we've already met the diversity quota, so no thanks. Besides, we don't want it to be too "political" and lose our dependable fanbase.
All studio execs do is "mitigate" movies to appeal to a broader audience...
An analogy would be a corporate chef who removes garlic from a tomato sauce so that people who don't like garlic will eat it, and those that do will know something is missing but can't complain too much because... endless salad and breadsticks, plus mom likes the "atmosphere"
Replace garlic with trans character, and endless salads and breadsticks with the MCU
I can think of one reasonable reason for it. They'd be harder to identify between the two versions. It makes some sense to not change the look that much (or the actor if that was the plan) to not confuse the audience.
I mean you credit them as 2 different roles, Switch (In-Matrix) and Switch (IRL). Happens all the time for different ages of the same characters being portrayed by younger and older actors.
The more I think about that, the less I'm sure how it would have worked. Any interpretation has knock-on effects for the sci-fi aspect of the premise. (Less of a problem for the philosophical and filmmaking side of things, where it's often fine to say "fuck you, deal with it.")
If Switch in the matrix is physically female but androgynous trending butch (kinda like canon), while Switch on the Nebuchadnezzar is plainly played by a dude... is that Switch being FTM? The character's deepest internal state, behind the false system of the matrix, is a dude in a bucket. Maybe their presentation (via the body the matrix slots them into) is limited to a haircut, because who cares what your avatar looks like? It's not you. Take your Fortnite default skin, get on with the mission, and get back to reality.
Obviously the more-likely-intended take is that Switch IRL is MTF, and gets to present however the hell she wants via the matrix. But that implies anyone could look like anyone else. If that requires some deep-seated self-image, rather than a malleable state only limit-breaking individuals like Neo can freely change, you figure Cipher would have hair. Or at least Mouse could give himself a couple inches. In one way or another. Even if it is only limited to modifications of your physical body, the idiot-proof shorthand would be a character who lost a limb during a squid attack still having it in the matrix. There is the image, the body, and the mind, and the body is overall a shite vessel for conveying the image from the mind.
Anyway, the funny version would be to cast a brother and sister for the separate parts (phrasing) and never mention it. Maybe Neo gets a double-take during the rapid-fire introduction to the crew. Not so much as an "Oh."
It would be easier just to use an androgynous actor and dress them female in the matrix and male outside. No need for two actors, and it would be easier for the audience to remember the were the same person. Give them a little piece of styling that's unique and consistent between both, and it wouldn't be an issue.
Doesn't everyone on the Neb dress kinda the same? It's all raggedy gross makeshift cloth. And then in the matrix it's all leather dusters over fine linen shirts and rugged pants... except for Trinity and the gun show.
Sure, but like, all you gotta do is give them a hat that they specifically had remade in real life because they liked it so much or some shit like that.
Come to think of it, it's kind of odd they didn't give her Apoc's white shirt. Everyone else's color scheme in the matrix is kinda black-on-black, varying only by matte black versus shiny black, except for Morpheus's tucked green tie.
If the franchise had gone very differently, and explored the tech more than the philosophy, there'd be people with wholly different personalities in and out of simulation. They are literally online personas. If this had spawned a TV show instead of two-ish sequels, there'd be awakened hackers who spend all their free time in their ship's construct, and barely function outside of it. Basically the antihero version of Cypher's path: they recognize the necessity of defeating the machines, but long for modern comfort. They heard about people rejecting the matrix 1.0 utopia and said "I would just not let that happen to me." Once Zion triumphs they're gonna retire to some lotus-eater solipsism. Anyway: it'd fit a character named "Switch." Maybe give her the only vibrant colors in the crew's wardrobe. Or at least dazzling patterns. Turn the contrast with her all-white getup into multiple forms of contrast.
But that implies anyone could look like anyone else.
I would assume the machines hook the brains up into the matrix, generating the body based on DNA and what the brain expects, not based on a scan or something. Which would mean that in the matrix there's no trans people because noone has a body they don't vibe with but it also means that you can't just wish yourself to grow a couple of centimetres or such.