I've been both a huge fan of the Epilogues from the get go (with some minor grievances about some specific happenings in the later parts of both routes, but coming out of it having tremendously enjoyed the bulk of it) and a huge fan of happily transmasculine/happily non-binary (defeminized sense of self despite pregnancy, it's legitimately awesome nuance) Roxy when it was happening within the comic.

I saw the discourse online (on Twitter specifically) about how it decanonizes the long-implied trans woman coding people have gathered throughout the years, and I thought it was very weird to not just accept that characters aren't trans "in the way you personally want." Years later, I do view my past thinking as somewhat reductive. There are regular transphobes, pieces of shit who argue for years that no character in any media is transgender whenever anyone indulges in the thought, and then there are intra-community transphobias of people who apply any type of biases towards fictional characters the way they would do for real people. Transfeminine Roxy could've been enjoyed by a large majority of trans homestucks, because of the chromosome characterization (Ro-Xy name reveal being in two distinct steps, establishing a certain importance to the letters XY, that is then confirmed by Hussie herself here to be a direct subversion for both Roxy, suggesting their transwomanhood, and Dirk, suggesting his transmanhood, which is very fucking funny in retrospect : https://wheals.github.io/formspring/formspring.html#andrewhussie448980558)

Both Johnny and kevin (https://fruityrumpus.com/forums/reply/689c0fdec24c58e653acb193) have pointed out the different ways these trans coding were not exclusively transfem but transmasc as well, and generally I do like a good arc of compulsory hyperfemininity being challenged. I'd very much like to hear about the pre-epilogues transmasc coding of Roxy, as I've never heard of it before, it's great that it was a thing already !

Also Johnny's take on both transmasc and transfem Roxy being able to coexist (https://fruityrumpus.com/forums/reply/689c01f1c24c58e653a844b5) is obviously a good & real one since well, Homestuck, even pre-epilogues, has always been a story of dubious canonicity. Most people engage with fanfics more than they engage with the original material, so naturally everything is possible including probably the shittiest fucking AU where everyone is cishet, which I would naturally not wanna handle even with anti-radiation gloves. Speaking of radiations, there's even that very popular one people enjoy where john sees dave gives birth to john.

[Unimportant rambling - you've been warned. Skip at your discretion]
Anyway it did lead me to wonder why they couldn't have gone further with less grounded paradox space gender shenanigans. What if both transmasc AND transfem Roxy had been a thing in the epilogues ? We did get transmasc AND non-fem non-binary, but what if their void aspect had interacted with the fragilization of a solid canon itself ?
What if they were transmasc in one route and transfem in the other ? (Given they're clearly gnc and fluid in both routes, wouldn't have excluded any type of non-binary). It would've been very Homestuck-y to have a Roxy that was paradoxically more "AMAB" Transfeminine AND "AFAB" Transmasculine depending on the route, and all that could've been even more of a cool exploration of gender I think. I do like the pregnancy talk in candy but I do think it could've been more trans. Like why was the pregnancy specifically enough to not have him be a trans dude, to the point where a lot of people seem to be seeing him as cis in that route ? (Roxy is never cis to me, I thought it was explicit enough but a lot of people, even trans-friendly ones, took the pregnancy bit as them being cis somehow..?) I think there's still too much taboo around explicitely masculine trans people getting pregnant, and Homestuck's ironic tone could've definitely approached the stuff in a funny and insightful, pop-referential way (like the whole Mpreg meme, defusing its limitations and the fact that it's usually considered a joke even in queer circles, to the understandable discomfort of some trans men). Like the fact that "mpreg" or "male pregnancy" wasn't even a part of the overwhelming list of content warnings still strike me as a huge missed opportunity. It would've made the transphobes even madder around Roxy, and would've also been the opportunity to have an "AMAB"-coded Roxy in the other route, written specifically with transfeminine experiences in mind. Just spitballing here, as I said I love the epilogues as they are (believe it or not-probably more than the original material).

[Quick(?)(no nevermind) responses about other trans characters]
-the one and only June Egbert is obviously really exciting, but I'd be lying if I said I was very patient about her reveal. It's been years, and I do take in mind the several years of harassment & smear campaigns halting the production of any homestuck content and harming the livelihoods of some of the writers (in heavy transmisoginystic abuse, to keep track of the transphobia of homestuck fans). But the fact that it's been confirmed to happen before the Epilogues makes me think it wasn't really a priority even for the work that was supposed to be the (un)happily ever after point of Homestuck, establishing closure. That was one of my main grievances (along with Feferi's treatment, since I'm probably the number one Feferi fan and think she did nothing wrong ever)

-Eridan's pesterquest route was literally one of the best ones. Especially after the way Feferi was treated (can you tell I like Feferi) as a point to deny both Eridan & Gamzee fans the redemption of their faves, the writers had to distastefully add in sexual harassment jokes for some reason, when having an actual heart to heart between Eridan & Feferi could've been good either way. If you didn't want Eridan to change, fine ! I'm more than okay with it, I hate the character. But you could've unpacked his feelings of entitlement by having him be threatening, scary even, instead of making it a big joke that's ultimately at the expense of the female character getting forced to kiss her murderer. So seeing HIM finally get a setting where the story was actually unpacking some of it, within a funny route that (Homestuckingly) mixes pop culture references with earnest character development, it was amazing. I loved the Eridan route, and I loved the trans subtext of it as well.

-Sollux is peak, always has been, obviously transmasculine, the dude's chill as fuck and one of the only friends who help Feferi in the original comic (yeah that's my metric of inherently Good characters in Homestuck.)

-Vriska..............is also inherently Good under my Fefriend Meter, they have one cute exchange that's quite literally the cutest, fluffiest exchange Vriska has with anyone in the entire comic and that's saying something I think. I don't like the meme "[x did nothing wrong]" because it's a direct reference to Hitler memes, but the people who argue Vriska is scum are usually an adjacent kind of evil (Vriska having turned into a receptacles for lots of transphobic, and misogynistic sentiment festering within the fandom. These people gotta chill way more than the ones viewing her as being on the side of good-which she explicitely is in canon)

-Jade.....is Jade even trans ? I like her a lot, she was my first favorite character (Fefriend Meter : Beep Boop Jade is Inherently Good)
I think it's safe to assume Jade is transfeminized. The transfeminization being so powerful that she's been considered both "ruined" for having that "trait" "imposed" on her, the way most people talk about it. They're not wrong, it was definitely a narrative choice. But it also gets very interesting because it does touch on many aspects of the perception of transfemininity, including the uncomfortable promiscuity, the whole scandal of cheating somehow pushing her status as a disgusting, irredeemable character (or alternatively, hating the text or even the writers for having dared "tainting" her character), the general lack of understanding of how her canon years of loneliness might've done that to her (most people associating that to her having a penis, with what I see as a little confusion between correlation and causation - but the writers might not have had the wokest ideas either, I don't know. It's complicated, and that's what makes it interesting.)
I do love Jade, including in the epilogues. I think she's touching despite it all, despite her awkwardness, despite her fumbles. She's good.

-Dave and Dirk are trans men as well to me. I like to see both Striders as inherently masculine, I don't know if anyone has envisioned transfem Dave or Dirk, but to me they both have very dude problems, specifically with irony and control. I don't have any strong feelings one way or another, cis or trans, I do like the idea that Dirk technically trans but doesn't like the term and looks down to anyone using it (https://fruityrumpus.com/forums/reply/689c150fc24c58e653ae3467). A pattern I enjoy a lot with him is the whole blurring of conservative/progressive ideology, and so I would absolutely see him argue against the entire concept of transgender people from a radically leftist angle of rejecting imperialist language that has shaped our entire LGBT identities around medicalist & psychologizing assumptions, erasing indigenous cultures via genocide and forced assimilation to american customs of sex & gender, and boxing all that in a shiny, capitalism-friendly set of beliefs improving consumption rates within queer & marginalized populations. Naturally, Dirk being Dirk, he would then call someone a "passoïd" or something, showcasing his hilarious hypocrisy Terezi has been studying within beyond canon.

Damn. I wrote significantly more than I thought.
To conclude on all of that, transphobia is still overwhemingly a dominant ideology in society, and there is no fandom or community (or even political parties/militant groups) that escape this. Consumption of any "progressive" media doesn't make you woke, and calling media "progressive" is more often than not a reach. I've often felt weird at people..overplaying the queer representation a bit in Homestuck, especially when it comes to congratulating the team for June Egbert "existing"(character that has yet to reveal herself, after all), prior to any characterization she might carry the legacy of. As of the latest update, John is a socially awkward, uncomfortable guy who reveals he's emotionally cheated on his wife with someone he didn't know the age of, which for many can be read as a weird way to delve into a transfeminine character (see obsession around Jade's cheating impulses, and naturally the real-life instinct of many people -including within the Homestuck community- to treat trans women as pedophiles.)
With that said, scourge sisters & rosemary are right here for really incredible lesbian ships, but in terms of trans representation, we can still read all of the comic in a very perisex/cis-centric lens without missing much. (candy route Roxy being seen as cis by many fans, June being nowhere to be seen except in a little flash silhouette as of very recently). Obviously, things will get more trans from here, but when discussing transphobia it's also necessary to be critical of the way trans lives are depicted. I am somewhat wary of June Egbert, especially if not written by a trans woman. We should condemn transphobia within the fandom, but we should not let transphobia in the writer's room either if it happens.
We will see how it goes.