The closest I'm getting to understanding all this is that the trolls had a similar John Fights The Denizen timeline-dooming incident, where an aspect of the doomed timeline is part of the alpha timeline. I think what we've been seeing with all the trolls dying has been part of the alpha timeline, but in the doomed timeline they ruined their universe seed by not prototyping at least one of the kernelsprites, so upon beating the game they were trapped in a null session only this time without Jack or the humans around. Then Gamzee did kill everyone. And in the alpha timeline he is only partially successful.
But, you know, I have no idea. Until we get a formspring, what's actually going on is totally beyond me.
e- Oh christ, you know what? Doc Scratch isn't obligated to serve anyone; he's serving of his own will. The 'serving a demon' thing isn't a standard part of being a First Guardian, Hussie made that clear in his formsprings back when we found out Lord English was a red herring demon. So what would a Cal-created being serve, who we know to be a time traveller? I'm thinking Dave, Bro, and Hussie are all options here (the latter being unlikely but not out of the question, and the former being my best bet). We do have a green-suited dead Dave in a dream bubble.
God I feel so dumb for typing that out but an ide/theory must be spoken.