They absolutely do. Bonucci has almost exclusively played in a 3-5-2 with the same two other CBs for both club and country.
Take Miranda as a recent example. He was the hottest CB 2 years ago but is now at Inter (not bad but a step down) and is out of the limelight at only 31. Then look at Savic. Couldn't cut it at City, went to mid-to-upper table Fiorentina and did alright and is now 2nd fiddle at Atlético. Despite playing few games he still slots comfortably into the side. Every CB at that team seems to do well and that's a lot to do with how they train and how they play.
City haven't been so comfortable at the back, the PL in general isn't very forgiving on new players. They're not bad but they're no Italy or Juve at the back. Perhaps Pep's tactic will sort them out and perhaps he needs someone like Bonucci to do that. I can understand why Pep would want him. It was easier to take over Bayern because they were already comfortable pressing up high and keep possession but City, as good as they are, aren't Bayern and it will be a lot more comfortable starting out with a team that's solid at the back.
I have my doubts because I dont' see Bonucci as being the Pep type. I suspect Pep will do something different with City than what we've seen before. Maybe something a little more "boring".