I think it's a fictional universe and as long as you confine your take on it to your AU and your games, no worries.
But, as for the Clans as a whole...
TLDR: Rather than being a fertile field for those on the LGBT+ spectrum, I think the Clans are more likely to be a fountain of sexualized evil and in fact; quite down on the variant gender expressions we see today.
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I've been looking a lot at the Clans and their cultural development for my Der Tag AU and I'm not sure all that sunny an outlook is likely. I take pride in a realistic approach to the setting and the Clans are a whole bucket of bad news for anything and everything sexual. In Der Tag, I have to have them go through a transformation to a stable state that is not going to just be a factory for sexually-abused/abusive psychopaths unleashed on battlefields, because I think we've seen the limits of what can be done with that in the failed invasion.
The most-recent study IRL I am aware of indicates that sexuality has both genetic and environmental markers. The environmental portion will be most unkind in the Clans.
I think if the Clans could have just edited out sexuality from their trueborn breeding program, then they would have. The writers certainly left enough weirdness in, so that was a choice, likely for relatability. Go read Haldeman's Forever War/Peace/Free to see what a masterpiece of alienation you can produce by creating a universe designed *not* to relate to the reader.
I sincerely worry for the future of the Clans as a faction, if this is a rabbit hole TPTB go down, because as-is, they have created a culture shockingly likely to condone and normalized sexually abusive behaviour at all levels. Frankly; with the normalized putative incest of the Sibko program, it's bad enough from where we are now.
Looking at the Clans, I think that gender is something that is going to be more or less irrelevant to them and in a very negative sense. A Clansman (gender-neutral term) is going to see themselves not as man/woman/other, but as Warrior/Scientist/Merchant/Tech/Labourer. Achieving sexual gratification and physical attraction will be secondary considerations. Some are probably even effectively preferentially-asexual through a rigorus regimen of self-denial.
Within that spectrum, however; what we would relate to as pan-sexuality, or alternatively: an attraction to competency or achievement would be much more common than what we have now.
That's fine for peers.
It's less-good for subordinates and lower-castemen (gender-neutral term), where the Clan-system is wide-open for abuse. Now, it may be arguably written as culturally-frowned upon (but I've read all the original novels and a few SBs and I don't see that in place at all), but in the Clans, rank seem to 'hath it's privileges and these will be weighed against the social and practical counter-weights of saying "no" if a person wants to.
That comes in to this conversation when your superior in rank or caste wants to get off and you don't want to help them. Clan culture is going to thus lean to a balance where one's own gender and preferences are less-relevant to this situation than your station in life. So at that level; I think the Clans would be a "Hole is a hole" people with a heavily caveated understanding of consent.
The implications for the trial system are disturbing.
But the OP mentioned surgery. Probably not.
I think that any Clan would call that a waste. Throughout the books we have many references to Clansmen of all castes looking at nearly any degree of extraneous attention to one's appearance as a disgraceful vanity and that attitude will extend to any form of body/gender dismorphia being treated as an example of a genetic/mental defect. Such a person will be quickly consigned to Dezga status, solahma or even the dark caste.
But...what about a trial for it? Maybe. But there are going to be limits, stark and low-bar. Clan medicine may theoretically trump anything else going, but it will not practically extend to anything cosmetic. Your body needs to work to serve the Clan, not your psyche and anything that compromises that needlessly will be prohibited. The base MedTechs will be able to handle skin-grafts and maybe cloned limbs and internal organs, but not gender-afirming care.
The Clans probably aren't even going to be practical for cross-dressing, due to how they value conformity and are generally down on extensive personal possessions. A culture that doesn't have time for physical beauty won't have time for anyone's unusual wardrobe, either. But if your dress is practical? Maybe. Merc units or Solaris are better options. As far back as MW1 (the game), we had NPCs who wore gimp-suits in the cockpit and Sorenson's Sabres (Kurita regulars) gave us Vernon Morrone, with his 24/7 full-face mask. So there are indications that there is more tolerance there.
I considered writing more about the Sibkos here...but I'm just not up for it. This stuff takes it out of me.
Suffice to say that from just what we have in the Jade Falcon books, the Sibkos are a factory for monsters. The whole system is rife for abuse. Particularly when looked at through a multi-generational lens and maybe that's part of why decent warriors don't want to go there as staff. Gender Identity and sexuality in the Clans is something that is going to be shaped for Trueborns in the Sibkos. Revoltingly often by their instructors. We see this with Joanna and Aiden in the Jade Phoenix trilogy.
Joanna probably waited a lot longer than other Falconers would have before just ordering him to her bed. That this can happen at all in Clan culture has chilling implications, but it comes down to a culture where your sexuality and gender identity can be forcibly adapted to the situation by your superiors.
Apply the same notion to subordinate castes, but figure that "Slumming it" likely has social/sexual implications in the Clans comparable to slave owners taking privileges with their slaves throughout history.
It's not a good scene all around, but it may explain some otherwise inexplicably bad actors at any/all levels of Clan Society. One of the main limitations of human depravity being that people tend not to limit their depraved behaviour to one small aspect of their lives, but tend to be dysfunctional in other areas as well. Which makes the physical punishment and control of the trail system seem all that much more attractive as a practical tool. Consider further the implications for a system where even the very good actors feel compelled to turn a blind eye to these activities because "it is how it has always been", or "the system works".
So what I have done in my AU is to use the Warrior Caste and trials system to bring back a kind of stable family unit (and also a degree of petty nobility) to this corner of the setting to allow for the potential for reform and recovery in the years post-Jihad, without changing what the Clans are, conceptually. I still don't have a way to bring extensive sexual/gender identity variation into the Clans plausibly, but that hasn't been a goal for me, either. I did make Stone and Lear a couple though, so there is that if it matters to you. But then, my Magistracy's cultural zeitgeist is autogynophilia, so that may be a wash anyways.
Bottom line is that with the setting *as-written*, I would lament for the fate of any person born into the Clans, but particularly someone who feels trapped in the wrong body. Hell; "Trapped in the wrong caste" is no picnic, either. I'd imagine that the particularly-variant phenotypes have similar issues as-well.
Unless your kink (YKIOKWM) is a pansexual dominance hierarchy with a sexually-available underclass, where your own sexuality is subject to the whims of your superiors, the Clans are going to be pretty rough feed in that respect.
And if you're wondering how I got here, as I said; I read all the pre-dark-age novels, and a number of sourcebooks. I'm a student of human nature, including crime and indoctrination and I just took the Clans as-written, particularly by Stackpole and added human nature to that.
I'll book-end this by reiterating that if this is something important to you, then by-all-means have it in your games, your fanfic, your AU. The universe is here for you to enjoy and variant sexualities are going to be a part of an adult version of that universe. The novels being written to YA-standards doesn't stop us from extrapolating from known data. I am not against any one individual, but I am against retcons; so the negativity you sense here is that attitude; I don't want to see the Clans RetConned for any reason. I don't want to see any RetCons for any reason. I think that if we start applying adult logic and sexuality to the Clans, we are going to end up with a morass of evil RetCon-bait. To avoid that happening, I'd prefer TPTB steer clear of exploring this aspect of the Clans as-written.
