The Cybus designs were back the very next year? They're in series 6 after the Pandorica stuff. Then they're gone, admittedly, in Nightmare in Silver, but then they're back (alongside every other variation) in series 12. The lore with Cybermen is that the Cybus alt-universe Cybermen went out into the universe after the events of 'The Next Doctor' and eventually met with, joined with and mingled with the Mondasian one. The 'Nightmare in Silver' Cybermen are meant to be a 'new race' formed by the two uniting.
I guess I tend to block out post Season 5/6 Moffat for being pretty horrendously bad in my view. It still doesn't explain Jack's reappearance and knowledge of the Doctor though, or the fact that a multiverse theory overarching plot would've been better and/or made much more sense than whatever what just happened was.