Disturbing Insane Theory: The human characters also arose from incestuous slurry.
1: PreScratch Reckoning meteors enter PostScratch Universe
2: PostScratch Jane ectobiologically combines John and Jade to create herself and Jake, Dave and Rose to create Dirk and Roxy.
3: PostScratch Reckoning meteors enter PreScratch Universe
4: PreScratch John ectobiologically combines Jake and Jane to create himself and Jade, Dirk and Roxy to create Dave and Rose.
5: See step 1.
Assuming the same thing happens with the trolls, this resolves the weird asymmetry in their Scratches, and gives Hussie that punchline about incestuous slurries.
Might contradict the nature of paradox clones, though. Depending on whether or not you can have intermediate paradox clones count toward that bit where a paradox has to be genetically identical and ultimately become the person cloned, since this necessitates that the instance of a given character created ectobiologically be different than the source instance.
EDIT: Also, arguably, contradicts the end of Descend, in which we follow the path of the meteor that strikes John's house, unless only meteors bearing a child swap universes. Can't be Jane's, because it's not autumn in Descend.
EDIT: Oh, wait, nevermind. Also contradicts the artifacts they bring with them, something I kept bringing up myself.
EDIT: Damn, now I don't even know what to think. If there's only one copy of each artifact that loops through each universe, that would work. It'd require that they all wind up in the same place, but preScratch John's book being so beat up would make sense if it aged through the postScratch universe instead of just 13 years preScratch. The tiny Maplehoof might be a clue that postScratch Dave made more of them, and if a full-sized one gets pulled into the Medium like the original Maplehoof it might be a case of two otherwise identical creatures; Dirk obviously has access to some sort of captchalogue tech, given his request for a ghost imprint of a brain, so this isn't entirely ridiculous. The hat and dirty bunny are already beat up enough that aging isn't necessarily going to make them noticeably worse off. Cal and Mutie aren't terribly old given that Bro and Mom are relatively young from the look of things, and whatever happened to put Mutie in a block could explain whatever longevity is necessary for it get through to the preScratch universe, later to be freed by Mom.
The knit bunny and the pistols, we haven't seen postScratch as far as I know, and the bunny in particular is probably going to be wonky due to going back and forth between Jake and Jade anyway.