Matt VDW,
I'm not intimately familiar with the CZ/Witness, but I am with USPs. The way you describe the action of the CZ, it really is not and should not be used as a double action gun, even though it can be fired as such. My duty carry is a SIG 229, and, as noted, after shooting, you decock and holsster a "safe" weapon. This drill is performed this way because this weapon is designed to be carried as a double action gun. The CZ, like the 1911, is designed to be carried in SA mode, it doesn't seem to me that it would make sense to carry it decocked-it should be carried, and reholstered as a C&L SA gun.
I own and love a V1 USP, which has both decock and safety on the lever. I've heard it said that it is quite likely that when drawing C&L under stress, one can hit the lever to go off safe too hard and decock-not a fatal mistake as you can still fire, you just lose the SA accuracy. I'm seriously considering changing to V9, which is intended for true SA operation, even though it will still operate in DA.
The last sentence of your post hit the nail right on the head (at least for the V9 USP), in the USP manual on page 9 it states that the pistol can be carried in DA mode and provides second primer strike ability to SA shooters. I personally feel that the CZ and the V9 USP should be carried as SA only pistols C&L and the DA function should only be used if there is a hang in the chamber. There is also an excellent argument to be made for just racking a round out if the primer failed on the first strike, rather than pulling the trigger again on a failed round.
The most important thing in all of this stuff is to be intimately familiar with the guns you own and use, whether you carry them daily or not.