i suppose having enough of the alpha kids as trans would probably mess with the ectobiology since if all of them were XX then i'd think shuffling to get male bodies would be, er, impossible? but the quick and dirty answer to that is, one, it's imaginary science and may not even involve chromosomes at all, and two, don't poop on people for it! looking at you cherubplay person.
i understand what you mean though, about things like that. i mainly get weird about headcanons when people INSIST they are canon and use evidence that hardly counts (i fight people over "jake is canonically short look at his body sprite" because there are no canon body types in homestuck either), but i think i've played literally every character in the book as trans at some point. i stopped being weird about nonhetero characters when someone told me i couldn't and i just said watch me.
Yeah if someone wants to explore what ectobiology entails and what they think is and is not possible, that's great fodder for fanfic! Pretty awful for using to squash other people's headcanons with in RP. If you (general) get that controlling about other people's headcanons you should really think about sticking to fanfic rather than trying to strongarm other people into playing pretend your way.
Oh MAN does that My Headcanon Is Actually Canon Because Flimsy Reasons attitude grind my gears. It's controlling bullshit like RP dude is doing, but trying to wrap itself in Objective Rightness, or if it's a representation thing, Good Person Points, leaving people who disagree with it to feel vaguely guilty for what amounts to no good goddamn reason. Yay!
Three cheers for spite as a great motivator, though! :D IT's a good thing to hold onto when you're getting a lot of "No, you can't have or even create the representation you crave." JUST WATCH US.