Not really as I said time ripples. The game board is already new so don't expect how things transpired in the main timeline to much matter.
While the desired effect may be the same, time doesn't really ripple according to these movies. It sort of ripples but mends itself. The writers themselves have said that many things remain constant. So technically it doesn't really follow any rules except to follow the whims of the writers. Like I said, the effect is the same. They could easily say X happens to Botany Bay, where X can be just about anything, and they lean on that crutch.
It's hard to say what events could have set things in motion from a logical point of view. They should probably flesh out the back story quite a bit if they go some crazy different route with it.
I'd like to see Khan as head of an empire with augment troops to boot and an actual face to face off between the two at the climax of said film.
It sounds interesting, but is it even plausible?
You can't state its really up to the whims of the writers and than ask if its even plausible. By whatever logic they care to get there, it can be made to be plausible.
Speed of plot and all.
There's decades worth of time plus a fairly smart guy who given the resources could build himself a smallish empire and who knows what sorts of tech he's pirated along the way. Given this would be a not so insane Khan and all.
I'd love to see a fleet of Botany Bay class ships equipped with warp and phasers.