For what it's worth, I think Beyond Canon's recent update is addressing the very complaints you have, which is the idea that Canon is something that will always override any popular fanon depiction of a character's story. I know a lot of people hate the Epilogues for pretty valid reasons, but I enjoyed Calliope's depiction because she's the only character who pushes back and agrees with the "Fans" (the nebulous conglomerate of Readers who read Homestuck and stuff lol AKA Us.) She agrees that just because something is "fanon" and doesn't "matter" because it doesn't fit into Canon's strict framework, that doesn't make it any less impactful, because it still affects people anyways.

And the recent update, which idk if you've read but which was really good IMO, sort of introduces this new idea that fanon is equal to canon when it comes to Homestuck, and that the story can be molded by average people who just enjoy the story.

There are other things I have always speculated about the Epilogues as well, like how Dirk has some sort of soft disdain for John simply because John is the main character and thus has all of this narrative importance that Dirk will never actually get. In Meat, when John dies, he speaks very coldly about John and even makes it seem like John was always insignificant and like he can't understand why someone like us (the readers) would even be worried or sad about John dying off lol. But the truth is that John is a character who's relatable and important to a lot of readers because he's a character people have grown attached to. Without John there really IS no Homestuck, and Dirk doesn't really "get" that. He doesn't get how someone like John could be given such power just due to fans who like him in a story.

In a sense, "fanon" is the reason John is still around not "Canon". It is because of fans that he's the main character 15 years later, basically. And that is important, it's like that whole death of the author shit.