I never took those explanations as particularly set in stone tbh. Gender doesn't have hard rules, so anything that is tied to them by default also really doesn't. I always took it as Calliope just having a binary view of the world, one Cherubs are just wired to possess, and one that she distances herself gradually from.

I will say, tho, that the gendering is probably carrying over for the Jungian archetypes which inspired the Homestuck classes to begin with. Stock characters as a whole are very gendered (prince charming, evil hag, damsel in distress, etc.), but experimentation with the base ideas they offer are at this point as the original ideas themselves.

And while, again, I do not believe gender has any hard rules, it would certainly be interesting to see explored what it means, in the context of Skaia's narrative, to be a male Witch or a female Prince, for instance. One could simply take the verbiage of the Class and apply it, but the Classes are not simply about powers. They are, still, stock characters of sorts. So, is a female Prince a Princess? Or is a female Prince more of a "woman in disguise" kind of trope? What does that role look like in the narrative of Paradox Space, and the story being told?

Additionally, what could that mean for a character that has transitioned? What would June Egbert's "Heiress of Breath" be, if it'll even be. I do not think she'll become a different Class entirely, but her experience as a Heir of Breath will probably change. That is not necessarily connected to gender, but is also not not connected to it.