I haven't read problem sleuth so i can't really comment on that, but that's why i compared it to Celeste. Theres obvious trans themes in early homestuck, in the same way that Celeste is a trans story (and also the Matrix for that matter). But at least for Celeste, the woman who wrote the story and wrote Madeline as a self insert with a lot of the same issues did not know she was trans at the time. She realised it before finishing the DLC which is why farewell has the tiny trans flags in it, and the entirety of Celeste is a trans narrative, but especially the non dlc part is an egg narrative. This might also be true for the matrix, i dont know when the wachowski sisters realized they were sisters.

I don't know what the correct words would be to describe a story like this, but I do feel that the main homestuck comic is more of an egg narrative than a trans narrative, if that makes sense. The epilogues and beyond canon do get a lot more explicit with it, and this might be why