It's probably a combination of both. I think some catchers do genuinely prefer a certain way that a catcher receives the ball, etc. even though another catcher might be just as good defensively.
In the case of Leon and Vaz, I think it's probably the result of the comfort level growing from being paired with a specific catcher, but that's just a guess based on both catchers' ability to handle pitchers well.
However, if you have someone like Salty (no offense to him) versus Vazquez, then there would be a genuine pitcher handling preference.