In the 90s anime they are men that turn into women when they are senshi. It's unclear as to if they just became men when they arrived on earth (Their princess makes reference to Seiya's earth form being different) or if they were always men on their home planet and only women when senshi.
In the manga they are always women who dress up as men to disguise themselves.
To rehash the above, they were in the guise of men in both continuities, in dress alone in the manga and more corporeal in the anime. They were still women in both continuities and are so under Naoko's female-only rule that Sailor Guardians are only female. She did state the physical disguise in the anime was going against her rule.
On a side note, as there is no female royals for Earth during the Silver Millennium era, this leaves Tuxedo Mask as a Star Seed holder, but does not have the same designations as Sailor Guardians.
1. Naoko never said there was a "female-only rule that Sailor Guardians are only female," nor did she say the anime's change went against that rule. All she's ever said was that all the Sailor Guardians were female in response to questions about Uranus and the Starlights; saying that all her Sailor Guardians were female is not the same thing as saying only women can be Sailor Guardians.
2. Tuxedo Mask has a Sailor Crystal, not just a Star Seed (everybody has a Star Seed; it's nothing special). Sailor Lead Crow says that anyone with a Sailor Crystal can call themselves a Sailor Guardian. Therefore, Mamoru could call himself a Sailor Guardian if he wanted to, it's just that he'd already invented his alter ego before awakening his past life memories. Still, he's able to transform and has special attacks, just like every other Sailor Guardian. He is a Sailor Guardian, just one using a different name.
3. Are we even entirely sure the Three Lights are posing as men in the manga? I feel like their public gender is ambiguous for several reasons:
--- In the Materials Collection, Naoko doesn't mention anything about their posing as men, which, as something that would be a pretty big plot point, you'd think would be included. Instead, she only notes that Seiya was inspired by famous butch lesbian supermodel Jenny Shimizu, and that Taiki is like a Takarazura star. To me that suggests that they're simply meant to be butch women (not unlike Haruka, whose MC page also compares her to Takarazura stars), not women pretending to be men.
--- There's this illustrationNaoko drew of the Three Lights in obviously female clothing. Of course, this could just be a picture she drew for fun and not necessarily reflective of the Three Lights' canon identities, but it's still something to consider.
--- Naoko doesn't exactly have a lot of range when it comes to drawing character faces. She really just draws one face to be honest, and she distinguishes men from women by giving women feathery top and bottom eyelashes, and men only top eyelashes (generally not very feathery). When we first meet Haruka, and we see that the general public thinks she's a man, she's drawn like a man: no bottom eyelashes. The Three Lights, on the other hand, are always drawn with top and bottom eyelashes.
--- Usagi experienced much confusion with Haruka's sex/gender identity, frequently wondering whether Haruka was a man or a woman. That same confusion does not appear to exist regarding the Three Lights, and when they transform in front of everyone, none of them seems particularly surprised that they're Sailor Guardians and clearly female.
--- In Stars 2, there's that scene where Yaten criticizes Michiru's choice of lipstick. A bunch of fan girls then swarm Yaten, remarking that Yaten's a model and asking for makeup tips. It seems strange to me that girls would ask a male model for makeup tips, but I guess it's not impossible.
--- In the Materials Collection, Naoko notes that Yaten brags about weighing 84 pounds. I can't imagine a guy bragging about such a thing.
--- It's true that the Three Lights are always being swarmed by adoring fan girls with giant heart eyes, but that doesn't mean they must be a boy band. There are plenty of androgynous women that otherwise-straight girls have crushes on, so it could well just be an instance of that phenomenon. Minako even tells Rei, after they've all witnessed the Three Lights transform and definitively know they're female, that she wants to get a boyfriend who's hot like the Three Lights. If Minako still thinks they're hot and ideal, knowing full well they're women, why not everyone else?
--- In Stars 1, Minako describes the Three Lights as
女のコみたいにカワイイ夜天光！ The girlishly CUTE Kou Yaten!
アダルトな大気光！ The ADULT Kou Taiki!
そいでもってイチバン人気のクールガイ星野光ッ！ And the NUMBER ONE most popular cool guy Kou Seiya!
"Girlishly CUTE" and "cool guy" may suggest that she thinks they're men, but not necessarily.
--- In Stars 2, Usagi muses
Sure enough, those three REALLY are COMPLETELY different from the boys in our class... SO COOL
Comparing them to the boys in her class seems to suggest that Usagi thinks that they're men, but she could just be oblivious. At the same time, her "sure enough," "REALLY," and "COMPLETELY different" might suggest that she does, in fact, know they aren't men, and she's just thinking the obvious.
--- In Stars 4, Nyanko Suzu warns Usagi not to trust women who assume the appearance of men. She says this in full hearing of one of Usagi's classmates, and it's clear that she's talking about the Three Lights. The classmate says something like, "Eh? Whom are you talking about? Usagi, you're not a fan??" This could be taken to mean she doesn't know the Three Lights are female and is surprised at the accusation, or that she does know and thinks they're talking about someone else.
So yeah, I don't think it's all that cut and dry. If the Three Lights had worn a school uniform, there wouldn't be this ambiguity, but instead they just wear their regular old boiler suits to school.
--- In the Materials Collection, Naoko doesn't mention anything about their posing as men, which, as something that would be a pretty big plot point, you'd think would be included. Instead, she only notes that Seiya was inspired by famous butch lesbian supermodel Jenny Shimizu, and that Taiki is like a Takarazura star. To me that suggests that they're simply meant to be butch women
Valid points for sure, I never thought of it that way. Maybe it's just strange for there to be a "girl" band that dress like boys who girls would fall head over feet for (then again it's Japan), we all just maybe interrupted them as pretending to be male since they're drawn that way and act that way but in fact they never do claim to be male. I just think with that there would be some kind of .... dialog to address the fact that they are butch or that no one knows their gender.