I don’t mind the different interpretation but I don’t agree that machines would for some reason not have trans people exist in the matrix. Are we assuming they have the ability to assign someone’s “true” gender at birth? Trans women are trans women. Trans men are trans men. Simulating their genitals to be “correct” wouldn’t change that. What do they do with nonbinary people? Nonbinary people can’t be “tricked” to not conform to a set of binary gender identities.

Would trans or nonbinary people be more likely to question the Matrix? Sure, you could argue that. But so would neurodivergent people or anyone that’s feels they are not accepted by the social constructs of society. The reality that human beings accept and question the least is the reality that we live in. A reality where trans people exist. Humans (and especially trans/nonbinary humans) would be far LESS likely to accept a reality in which there are only two genders. It would make the matrix LESS believable not more.

I think you’re projecting the human history of attempting to erase trans people onto the machines. Which could be an interpretation. But I don’t see the machines as malicious or evil. I see them as logical in their methods of control.