Gender non-conformity =/= rejecting the gender binary, though. The whole point of non-conformity is accepting that interests, fashion sense, behaviourial patterns and types of sexual attraction aren't hard-coded to be rigidly masculine or feminine. Heck, what is considered masculine and feminine greatly differed between cultures and eras, with the modern rigidity being an aberration more than anything.
The idea is that one liberates themselves from the coding of how a man or a woman "should" behave under social pressure and just does whatever they want rather than conform to the notion that their non-conformity must mean they aren't the gender they are. At least, that's how I view it - hence my sometimes bitter remarks regarding the "accepted" perception of the concept that I caught a warning or two for (perhaps deservedly).
Somebody like beholders being hermaphrodites (male-identifying ones, though, apart from the hive mothers?) doesn't exactly serve as a justification for the more "traditional" humanoid races to base their forays into gender identity on. Although, I may have just given somebody an AU/character idea, so there goes that logic.
What you're saying is true that the two things aren't inherently inclusive from person to person, but from a broader, cultural sense they very much are linked quite inherently. Because in a world where gender non-conformity is the norm, then the gender binary as a concept would be negligibly impactful. I think that in a world where the commonly understood trappings of gender are accepted as just that, trappings, with no significance beyond aesthetics, then gender as a societal construct would be far less of a thing that people think and worry about. Which would mean that things like being trans would probably look different to our understandings. The gender binary as it exists today, I don't think can be separated from the rigid ideas of masculinity and femininity that society enforces. Because it IS a societal construct, and that aspect ofit is more impactful than any medical or scientific aspects. And trans identity as it exists today is deeply tied to the gender binary because at least in the west, the gender binary is enforced at pretty much every level. From childhood with toys and books, habits and patterns of behavior, colors and patterns, people are raised with strict expectations of gender thrust upon them from the word go. So of course when someone feels that their body is not the right body, they'll start by leaning into societal signifiers of the opposing gender because society so rigidly states that it's an either-or question. It's a complex question that I'm not fully qualified to talk about really, I lack both the academic depth and the lived experience to comfortably get everything across, and even now I'm actually holding back some stuff because I don't want to get too deep into this topic since now I'm veering away from the question of its value in the game itself.
Returning to the topic of the game then, I have thoughts on the place of gender identity, trans people, etc in the setting. D&D is different from things like say, the Witcher or Dragon Age (although dragon age also acknowledges the existence of trans characters) in that the setting was, from the beginning, made to be interacted with. It was always made with the intention of having players step into it. It's by nature, incomplete, waiting for the players to complete it with their own characters and stories. As such, there's a degree of oppenness inherent to the setting. It's not an enclosed world purely built upon the writer's imagination, there isn't even one writer, there have been countless through the decades. It constantly is evolving and changing. On top of that, Wizards of the Coast has made the conscious choice to push D&D as the quintessential ttrpg, the default, a choice that very clearly is working for them. They until quite recently welcomed players and fans to create their own content, to do things with the game that they couldn't or wouldn't or maybe eventually would in a different way. Now more than ever, D&D is about the interaction of what already exists and what its fans and players bring into it. So I think that given that outside context, it's not only reasonable and justifiable, but also in a way proper for the game's setting to include as diverse a selection of peoples as it can. Because the creators are already saying everyone is welcome, everyone can play. I think actively making room for lots of different types of people is important in that light.