This has zero to do with the magazines in any way. I can load a 9mm cartridge at max length 1.169 and it fits the mags just fine but it will never in this lifetime chamber in the gun. CZ barrels are notoriously short on FREEBORE in that the rifling starts very close to where the cartridge headspaces. Cartridges with certain wide ogive bullets, some factory loads and most commonly handloads that are not properly adjusted for the particular CZ barrel may not chamber in the CZ pistol.
You can run into some CZ barrels that are extremely short and some that are not. I just this week picked up a 3rd PCR and the chamber in this new gun is shorter than any other I have in that my handloads that fit perfectly in my other CZ's are too long for the new gun.
For the first time ever I'm considering having a gunsmith extend the freebore in the new gun.
Can't answer completely on the 9mm/.40 mags but the new compact mags are made to feed 9mm or .40 but I don't know that the older versions were able to do that.