Benatia can perform a sliding tackle, he can man mark a player, he can intercept an incoming player, he can be physical, Bonucci can't!
Passing the ball, does not make you a better defender, a better player maybe, but Nita better defender.
In a 3 man defense if a defense has two good defenders like Barzahli and Chiellini, a player who can pass, could be more valuable than another player who can defend and that's why Bonucci was preferred over Benatia.
In a two man defense, it is mandatory for CBs to know how to defend and in that case, Benatia is much better, Rugani too.
But spending 35mil to get back Bonucci only means that the 3 man defense is back, new BBC, Benatia-Bonucci-Chiellini