In the past it seems like every now and then someone would buy a new CZ and end up having to have the throat opened up/lengthened just a bit to allow more margin. Or allow them to use certain ammo that worked well in their other handguns.
I ran into the opposite one time. I was developing some new loads and pulled my P01 out of the holster, field stripped it and used it to set the overall length. Got to the range and the ammo wouldn't chamber in my M&P 2.0 5" pistol (with an Apex Tactical barrel installed). Just "assumed" the CZ would be tighter than even the Apex Tactical barrel based on how well the P01 shot (usual/expected CZ performance) vs. the M&P even with the better Apex Tactical barrel.
I guess it's a choice of 1. altering all your pistols to match enough there are no chamber length issues, 2. altering all your ammo enough to work in even th shortest chambered pistol, 3. having multiple loads and keeping them identified and separate so the wrong ammo doesn't get loaded in the wrong pistols.
By the way, never had issues with the CZ .40 S&W pistols. I've got a P09 .40, two P07 .40, CZ75B .40, and a Tactical Sport .40. Zero issues with any loads working different in different pistols. At least for the ones I have there's been no issues.