Since Naoko was a cis-gendered, heterosexual woman living in the relatively conservative country of Japan in the early 1990s when she came up with Haruka's character, she obviously didn't explicitly have the idea of writing a "gender fluid" or "non-binary" character in mind (only for a character who had both masculine and feminine qualities and for whom gender wasn't important), but the end result was a character who can and is today often read that way. Haruka doesn't switch gender presentations every day; Haruka goes through a long stretch of male presentation when we first meet them/her, then through a long stretch of female presentation that I think lasts through the end of Infinity, back to a stretch of male presentation in Dream, and finally another stretch of female presentation in Stars (we see Haruka wearing a female Juuban High School uniform). I think such changes of preferred presentation are fairly consistent with a gender fluid identity.
As for the character's 90s anime incarnation... There isn't anything inherently wrong with it. 90s anime Haruka is a butch lesbian, but she's not the most stereotypical butch lesbian either. There's nothing wrong with being a butch lesbian, just as there's nothing wrong with conforming to stereotypes in real life if that's who you are, but we're talking about the portrayal of a fictional character here, and an adaptation of a fictional character at that, and such portrayals are not accidental, nor do they exist in a vacuum. Naturally the changes to Haruka's gender presentation is going to elicit criticism from some fans, as will the butch-femme dynamic of her relationship with Michiru (see also: Kunzite and Zoisite). That's not to say the cishet characters and hetero relationships in this series don't have their share of stereotypes, but that's beside the point: In real life and in fiction, there are literally millions of examples of straight people and straight relationships, so perception of such people and relationships is going to be balanced. But when it comes to queer people and relationships, there is still simply not that much exposure, so there aren't alternative examples to balance out the stereotypical portrayals, and that can lead to people having possibly damaging misconceptions about queer people. That's not to say the stereotypical portrayals of queer characters in Sailor Moon are necessarily damaging/harmful, but they are part of a broader pattern of queer portrayals in mainstream media that warrants criticism. What Sailor Moon does that is damaging is the way it promotes heteronormativity and makes occasional, explicitly homophobic remarks, but that's a topic for another thread.