I think having a number 2 allows for a better man management style. Like your post says, and other reports have indicated, the number 2 is often closest to the player. The boss has to make tough decisions, some of which will not make players happy. In Rafa's case, or in fact any club with a big squad where not everyone is going to play each week, and therefore not always be happy, its useful to have a go between. Call it good cop, bad cop, or whatever.
Now the players should be proffesional and not need hand holding many will argue, but in the dynamic if human nature having someone you can go to talk things out, someone you feel is the players friend, is helpful. I'm not sure a skills coach can fill that role. Also the number 2, while being the friend of the player, is also directly involved in decision making, as the boss's right hand man. Again that's bigger than a coaches role.