I can't say that I agree with calling ANY pitch not caught by the catcher a ball. If it's obviously over the plate and obviously a strike, then call it a strike!
(Of course, I mean "obvious" to the guy standing four feet behind the plate who's job it is to be calling balls and strikes, not someone in the stands or dugouts.)
It is a fact that how a pitch is received- or, in this case, not received- can influence an umpire's call. Examples would include catchers who move up so close to the plate that they block the umpire's view, movement of the glove away from the plate to catch the pitch or catching the ball then yanking the glove back toward the strike zone. Any of those might influence the call on a borderline pitch.
I'm not saying that any of those should automatically equate to calling a ball. But when you're tracking a fast-moving object through a three-dimensional space, you're going to use every piece of evidence available make the call. On a borderline pitch, poor technique by the catcher can, in effect, tip the scale so that it's more likely to be called a ball than a strike.
But if it's right down the middle, obviously a strike, none of that should matter. In other words, on NOT borderline pitches...just call the obvious strike, not matter how the pitch is caught...or not caught.