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The problem is that even cutting edge saber guys aren't doing multivariate linear algebra yet. If CERA is to be measured...it should begin with the assumption that a catcher's influence on each pitcher will be unique and that we must look at each pitcher's battery pairs and then sum up the "partial stories"...while at the same time accounting for a blizzard of external variables (umpires, parks, strength of offense faced, etc). I have long considered adding the starting catcher into the mix of the F/S Matrix (which is a linear algebraic system that tries to plce credit for run scoring to the various pieces that can contribute...parks, umpires, starting pitchers, team offenses and defenses, etc).
That is the only freameowkr that will ever have any hope of figuring out the impact of a catcher on his pitchers.