By no means are they easy, but invariably Bonbon makes the worst "panic and jump in randomly" or "plant self to the spot and stick leg out" type decisions in those situations.
I don't think that's entirely fair.
He almost always manages to slow the player down a bit and allows the other defenders to recover somewhat before he makes the challenge.
If he was doing it really badly, Juve would be conceding a lot more goals from those situations and Bonucci would be getting sent off an awful lot.
For Juve to have their main CB to be such a weak defender is a worry, and having Pirlo pretending to defend ahead of him (he has an excuse being the playmaker) makes our spine very vulnerable.
I can't say the Bonucci bit would worry me all that much.
It would disturb me a great deal how often the situation arises where an opposition player is being allowed to run - pretty much one-on-one - at Juve's last line of defence.
The combination of playing a genuine three at the back, playing a presing games and - as you say - having Pirlo as the deepest midfielder does leave Juve pretty exposed when even relatively minor mistakes are made by players higher up the pitch.
It's another reason - one could argue - for the 4-3-3.
Keeping the two CBs nice and tight together so that they can cover each other may well give Juve more security than having the back three strung run across the pitch, and often with one of them pressing up the pitch.
Either that or you keep one of the wingbacks a little deeper (like Inter do with Zanetti) so that the CB on that side can play a bit narrower and keep things a bit more compact and reduce the likelihood of defenders being left exposed one-on-one.