Don't think it's got to do with ability as much as it has to do with the perception of Alex, not being able to create, hustle and run for a full 90 minutes in the way that Conte expects the team to do so.
I think players like Caceres who may not be technically astute, still have a better chance of being part of a set up like this. Even though Boriello is shit, I think Content is trying to figure if his physical presence in the middle would make any difference and that's probably why he won't play Ale and Quag together, while resting Matri.