A lot of this you have to take by what others, pitchers and coaches/managers, are saying about the player. When a player is highly touted in some way by the people who work most closely with him, there is probably some truth to it.
Outside of that, BP or somebody once did a study on catchers with a focus on how Varitek didn't get the defensive credit he deserved. This was before Leon's time, but the point is that analytics people are so good that they can take the data, and eliminate virtually every variable possible, thereby leaving no other reasonable explanation than the catcher's 'handling of the pitcher' or 'pitch calling ability' or whatever you want to call it.
We do not have access to a more recent study, but I bet the teams have access to some such study.