At AutoZone, at least the stores I've been at, every "grey shirt" has the safe code. But that safe also has an inner safe that nobody has a key for except the armored car company. Individual drops are each assigned a barcode, and when the armored car shows up, each individual drop is pulled from the safe and places into it's associated daily drop bag. If money is short, it's either because of a miscount (accidental or otherwise) by the individual who did the drop, or a missing drop bag (which typically ends up being found stuck in the drop chute).

There's a lot of bad things I could say about AutoZone. The level of accountability provided by the system they use for their cash drops, at least at the stores that use armored car services, isn't one of them.