I watched the fansub back in 2007 and haven't started my rewatch yet, but I seem to recall that there was still sexism, even in a world where physical sex is something everyone chooses. There was something, I honestly don't remember if it was in the show or an opinion I read in fandom shortly after, that some people (wrongly, of course!) viewed the choice to become female as "cowardly," because becoming male brought on the most changes, while becoming female was very similar to their default "maiden" sex. Also, the choice is irreversible once it's made, so people who chose to become male might feel "women's problems" don't affect them, and never really did, since their initial "maiden" sex wasn't really female, but undetermined. Plus whatever baggage inherited from back when they had sexes more like our world. Since all men are like that, they face no scrutiny or discrimination for having had female-appearing bodies before they became men. That's just a typical part of manhood in their world.
In some ways, I can honestly see it working out that way. In our world, the fact that no one chooses their birth sex can make a powerful argument against discrimination. But since everyone in this world is born into the same sex, and becoming a man or a woman as an adult is something everyone has to choose, it's easier to blame people for their choices, or act like they "opted into" sexism when they chose to become a woman.
As to why everyone doesn't just choose male, then: they may identify as women, they may not want the more extreme physical changes entailed in the male choice, or it could be a spite choice, like "Why should I have to?" I think the narrative is being openly critical of the sexism the characters have internalized, like thinking gallantry is masculine. The fact that there's social pressure to choose based on stereotypes could even have a reinforcing effect. (Which to be absolutely clear, I do not mean in a transwanky way--I don't think anyone, ever, has gone through real-world transition over stereotyping their hobbies or w/e--but transition in our world is very much marginalized, whereas voluntarily choosing a sex is mandatory in this fantasy world, everyone does it, and it isn't harder to choose one or another, so little things like being told your hobbies were always masculine when you happened to be of indeterminate sex might influence you when you had to pick one sex or the other with no biological card-stacking!) Because it's a choice and not really a biologically weighted choice, the social dynamics around it can get weird.
Though I do think that simply having female-like bodies must influence their decisions towards being female a lot too. Not universally, obviously, but it's familiar, it can become a part of their identity, at least for some people! It's possible sexism is justified as a sort of, "If we didn't add perks for being male, hardly anyone would choose it." Which I don't think is true at all (nor does the male/female ratio need to be 50/50 for a stable population) but it's something they might say.
Re: Simoun Rewatch - Episode 1 AND Episode 2
In some ways, I can honestly see it working out that way. In our world, the fact that no one chooses their birth sex can make a powerful argument against discrimination. But since everyone in this world is born into the same sex, and becoming a man or a woman as an adult is something everyone has to choose, it's easier to blame people for their choices, or act like they "opted into" sexism when they chose to become a woman.
As to why everyone doesn't just choose male, then: they may identify as women, they may not want the more extreme physical changes entailed in the male choice, or it could be a spite choice, like "Why should I have to?" I think the narrative is being openly critical of the sexism the characters have internalized, like thinking gallantry is masculine. The fact that there's social pressure to choose based on stereotypes could even have a reinforcing effect. (Which to be absolutely clear, I do not mean in a transwanky way--I don't think anyone, ever, has gone through real-world transition over stereotyping their hobbies or w/e--but transition in our world is very much marginalized, whereas voluntarily choosing a sex is mandatory in this fantasy world, everyone does it, and it isn't harder to choose one or another, so little things like being told your hobbies were always masculine when you happened to be of indeterminate sex might influence you when you had to pick one sex or the other with no biological card-stacking!) Because it's a choice and not really a biologically weighted choice, the social dynamics around it can get weird.
Though I do think that simply having female-like bodies must influence their decisions towards being female a lot too. Not universally, obviously, but it's familiar, it can become a part of their identity, at least for some people! It's possible sexism is justified as a sort of, "If we didn't add perks for being male, hardly anyone would choose it." Which I don't think is true at all (nor does the male/female ratio need to be 50/50 for a stable population) but it's something they might say.