Well, you're right to an extent. The stat geeks haven't been able to isolate "game calling" skills yet. Maybe a better phrase to use at this time is "handling of the pitching staff". I don't know whether you read Marchi's study or not in the article that I linked, but he explained this in a much more scientific way.
Basically, with the advent of PITCHf/x, the statisticians have been able to collect very accurate data on the other aspects of a catcher's defense - fielding, throwing out runners, blocking pitches, and framing. They have a very good handle on how many runs were saved or lost by each of those attibutes.
They also have a pretty good handle on how many runs each catcher was expected to have saved or cost his team. They start with that, then subtract the runs saved or lost from fielding, throwing, blocking, and framing. What they have left is attributed to what is thought of as the catcher's "intangibles", but often simply called "game calling".
To quote Ben Lindbergh from his wonderful article written about Yadier Molina's game calling skills, " “game calling” encompasses everything we don’t know how to quantify about catchers: the ability to soothe a pitcher’s psyche, to know when to make a mound visit, to spot mechanical problems and recommend fixes, or even to position other defenders".
And they do know that there is a wide variation in this "skill" between catchers.