I'd rather think Allegri is more concerned about Rugani's chemistry with Barzagli or Sturaro as RB, he probably knows is a big risk to play both of Sturaro and Rugani in defence at the same time...
Anyway, from my oppinion there is no real excuse for why Rugani didn't start any games since Fiorentina other than the fact that maybe Allegri is aware how weak our defending phase is atm and woudn't want to risk him becoming a scapegoat in case something goes wrong