"I think that part of it is due to a significant disconnect between authorial intent & fan interpretation of Homestuck as a work of fiction.
Homestuck is supposedly a deep, thoughtful comic about unhappy kids at the cusp of adolescence getting a chance to grow past the causes of their unhappiness & become functional adults with the power to make a new, fairer system and must earn the right to do so by undergoing a series of trials that force them to confront their flaws if they want to survive, and their trials are ultimately hijacked by another child who refuses to grow up and wants to make that everyone else's problem. On paper, this is a great concept for a story.
Homestuck in reality is an edgy, cynical, and mean-spirited comic that regularly plays favorites with the characters (with particular favoritism given to male characters over female ones) and is overreliant on real-world pop culture references that not everyone will get. The dialogue is extremely overwritten and the plot is padded, meandering, and needlessly convoluted & incomprehensible. The colors are eye-straining and it's physically painful to read it, and it takes a while for narrative payoff to occur if it ever does. It makes liberal use of racism and ableism, all of which is played for comedy. On paper, what's there to like about a story with this kind of execution?
In my opinion, that's the entire point of Homestuck. Look no further than SBAHJ: Homestuck is to us what SBAHJ is to Homestuck. It's an ironic webcomic that was deliberately made to be terrible to read and hard to enjoy because it was never meant to be enjoyed genuinely. Homestuck was, imo, only meant to be enjoyed ironically by cynical snobs who claim that there's more depth to their ramblings than there actually is and laugh at people they view as (literally) mentally-handicapped rubes who don't understand their genius and get confused or ragequit when the story takes a turn they didn't expect nor want. It's a comic for cynical, disingenuous trolls written by a cynical, disingenuous troll, and that was all that Hussie ever wanted it to be.
But in making this elaborate troll comic, Hussie unintentionally made something with genuine heart and care. The comic's popularity exploded in Act 5 with the formal introduction of the troll characters, which was (and remains) a very well-written xenofiction with compelling character arcs & worldbuilding. The very people that Homestuck was intended to mock quickly became the dominant part of the fandom, and I think this scared Hussie for reasons that went beyond some fans behaving badly. The very people that they dismissed as developmentally-disabled geeks found Homestuck good instead of rage-inducing. They were making observations of character & plot that she hadn't thought of. They were inspired to make their own Homestucks, and not only did some of these adventures approach Homestuck in terms of story quality some of them were exceeding it. People were rooting for characters intended to be little more than one-note jokes (Tavros, Sollux, Equius, Gamzee, Eridan, Feferi, and especially Nepeta) and wanted them to have more involvement, and some of their fans cared more about them than they cared about the characters Hussie cared about (Jack Noir, Vriska, Karkat, Dirk, John, Rose, and especially Dave, who was effectively Hussie's author-insert before Hussie put himself in the comic).
People were taking this ironic webcomic and turning it into something genuine. Hussie had two possible responses to this knowledge. Option 1, as seen in Galaxy Quest, would've been to become the mask and embrace the chaos that the fans loved. But that would require a degree of humility and honesty that I don't think Hussie is capable of, so they went with Option 2: alienation. He upped the deliberate bad writing decisions for Act 6, dragging it out with tiresome romance drama & angst and going to increasing lengths to depict their own fandom as idiots. The most notable instance of the latter is the characterization of the cherubs: Calliope represents the majority of Homestuck's fans, who find genuine enjoyment in it, and is depicted as a passive wimp whose only purpose is to die so another can get stronger; and Caliborn represents its critics and detractors who rightfully point out its flaws, and is depicted as a stupid misogynist who likes killing people. Keep the latter in mind, it becomes important later.
But despite Hussie's best efforts, more fans stayed then left. Collide failed to drive them all off. Ditto Act 7. Ditto the Epilogues. He grew to hate Homestuck because their "game" of using it to troll people they saw as dumber than herself wasn't fun to play anymore. But then they realized that perhaps having people genuinely believe in Homestuck wasn't a completely bad thing; after all, Hussie's never had a thick skin in response to criticism, and the surprising success of the Epilogues showed them a way to not only keep the fans they had & even grow the fandom, but to create an army to protect themselves from criticism and censor people who interpret Homestuck "wrong". The game of trolling the fans by pretending to care about the things they care about was back on, and the rule of this round is simple: representation via retcon.
One of Homestuck's biggest draws was its genuine lesbian, gay, and bisexual representation, which was rare at the turn of the 2010s and is one of the things it does right. But the political climate of the late 2010s was very different from when Homestuck started, and one of the biggest reasons was #metoo, which was prompting increased scrutiny of uneven power dynamics between men and women in media and ultimately increased scrutiny of any kind of bigotry in general. And Homestuck is, as mentioned before, a very bigoted work; even with the draw of LGB representation, its fandom would shrink and Hussie would lose money if people realized that being LGB was the only representation Hussie found socially acceptable, so Hussie started woke-washing Homestuck in an effort to make themselves look less bigoted than they actually are. This behavior has actually been around for a while, like the kids being "racially ambiguous" (No. No they aren't. The canon human kids were never intended to be anything other than rich white kids like Hussie themself; they're lying so they can use "you have the freedom to headcanon the kids' races as whatever you want" as a draw.), but it started ramping up after Act 7 and is most apparent imo in how Homestuck handles trans rep.
Roxy's gender issues were discussed in the original Homestuck, but imo poorly executed in the Epilogues and onwards, ditto Callie being nonbinary. Around 2017, June and transfem Vriska entered the spotlight. I don't have a problem with there being transfem Johns and Vriskas out there; the nature of Paradox Space means that there are billions of them. But I did have a problem when one fan used a toblerone ARG to "make June canon", because that to me reeked of an entitled Tumblr fan wanting to push their headcanon of their favorite character belonging to the same demographics as themselves onto everyone else so they can project onto that character even harder, not to mention how the fandom is now encouraged to both depict June as an inevitability for ALL Johns (which goes against Homestuck's own worldbuilding) and harass anyone who depicts John as anything other than transfem (perhaps even including cisfem) and call them transphobic. Something similar happened to Vriska being called exclusively transfem, with the added caveat that the person on the crew doing most of the pushing had Vriska as her favorite character and was very belligerent to anyone who criticized Vriska for being, y'know, Vriska. Recall what I said about Caliborn being a caricature of Homestuck's critics: Hussie wants the fandom to silence their critics, and retconning characters to be minorities gives them a way to do it. You can see this with RWBY too with how Bumbley was shoehorned into the plot specifically at a time when ratings and viewership were declining in response to bad writing decisions.
And now Jade & Kanaya are supposedly transfem too. Having Jade, the half-dog girl who cucked Kanaya, gave Rose a bastard daughter, tried to insert herself into Dave and Karkat's relationship, and spends most of her time literally screwing around is, as many others have mentioned, transphobic. But I really like the concept of Kanaya being transfem, because it adds depth to her struggles with her caste's niche of motherhood by adding a personal stake: if she succeeds in becoming a mother, she proves herself to be a real girl. The idea of not being "real" is something that trans people often struggle with overcoming, and seeing Kanaya find a way to overcome it would've been great.
Why do I think being trans works for Kanaya and not John? Because there's a way to fit it into Kanaya's character arc organically and seamlessly. John's arc never struck me as a struggle with gender roles, but a struggle with emotional maturity and the idea of being a "man" – not in the sense of being a "cis male" but in the sense of being a "serious adult"; John's entry item being an apple representing a loss of innocence supports this, so for me John being transfem doesn't feel as organic as John being a kid forced to grow up before he's ready to grow up does (autistic John fandom wya?). And while I accept that some fans can interpret John's arc as cracking the Egbert, I don't accept being told that my interpretation of John being a cisboy in the comic isn't valid either. (Honestly, Dave should've been the transgirl, his entry item is an egg and his sprite is half-bird, and Dove is right there the pun cannot be ignored.)
Vriska being transfem could work too if learning she was descended from Mindfang is what cracked her egg, and learning what a monster Mindfang was in life (or simply meeting Aranea) could make her worry that she's not a real girl because her role model wasn't a good person. On paper, transfem Vriska is a good concept. In execution, that's not what we get: we get a person on the staff encouraging the fandom to harass people who don't consume the official content "correctly" and weaponizing transgender representation to make said harassment seem just.
I promise this tangent is relevant to the discussion at hand, because this is an example of what someone who genuinely cares about Homestuck would do to incorporate trans representation into it organically. But it's this kind of behavior, looking for meaning & substance where there isn't any, that Hussie views as loathsome, that made them hate their own fandom until he realized she could weaponize it to distract us from his questionable decisions. I believe the intention was for the fans to destroy each other with name-calling and bullying until no one has fun with Homestuck anymore and gives up on it, but that didn't work and now we have the above drama in an attempt to hurry up the fandom's decline. Hussie likely thinks, as they always have, that we're too oblivious to see this, but once again they underestimate us. We can tell they don't actually mean the things they say about wanting more representation. Every long-winded rant typed instead of a blunt "Yeah" or "Nah" gives more evidence. And for me, nowhere is the evidence of Homestuck's dishonesty regarding representation greatest than its continued lack of genuine neurodiversity.
To my knowledge, Nepeta has never been confirmed to be genuinely autistic and no character has been retconned as neurodiverse, and I doubt that this'll ever happen. While Hussie can pretend to care about race while depicting the Condesce next to blackface in the same panel, and they can yell at John for saying the r-word in a very snarky way, having genuine representation of the [r-word]s that Homestuck was originally, and always, intended to mock is a line that Hussie cannot bring themselves to cross, because that's not a kind of lifestyle she regards as socially acceptable. Discerning intent is something that many neurodivergent people, myself included, have trouble with, and the evidence points to Hussie viewing this as a source of shame to make fun of us for, ultimately creating Homestuck precisely so we'd get confused about its intent and make fools of ourselves trying to figure it out so they could laugh at us with their forum friends and pat themselves on the back for being so clever in setting up such a trick. But it backfired, the people in the punchline loved the joke genuinely, and now, here we are.
In short, Homestuck grew past its authorial intent as an ironic comic meant to troll people who find genuine enjoyment in chaos thanks to the very people it was written to mock, and Hussie, unable to accept this, tried to alienate the fans who made them a legend, then tried to weaponize them to make the fandom destroy itself, and is now resorting to direct censorship and legal action in the hopes that someday, the only people remaining in the fandom are the cynical, disingenuous trolls that were meant to be Homestuck's only audience – because they'll be the only people allowed to consume it without fear of retribution. But once again, Hussie underestimates us. You can't fight the Homestuck? No. You can't fight Homestucks."