Here's what we do.
We use a system similar to yours - but as backup rathe than having to do things because machines have to be wiped - like you have to do.
We use dual firewire/usb drives from OWC with 4 partitions for the 4 setups we use in 10.3 and 4. The partitions are named for the correct machines - like "G4 103. We clone, with CCC, from a fresh computer hard drive, to the correct partition and install CCC on that partition. We make sure to include "hidden" files per CCC options. This was done for each of the 4 different setups.
When we do a reinstall from the outboard drive, we plug it in to a particular computer, and restart from the appropriate partition. We then launch Disk Utility from the outboard drive and erase the computer's drive using the Zero Out Data option - we have no need for any greater security but you might want to choose a higher level if necessary. We do get the other partitions mounted on the desktop but ignore them.
Once the computer's drive is wiped, we launch CCC from the outboard drive that's the startup drive and clone to the computers newly wiped drive - again making sure that "hidden files" are included. Then we copy the user and application files from either the g4 powermac that we use as a "semi" backup machine (server) or from the backup outboard drive that we have for each machine (double backup due to paranoia) to the machine with the new OS.
So far, we've never had a problem and did not get the override problems that you describe.. However, if this is driving you nuts, you might look into creating a disk image via Disk Utility and dropping that on an outboard drive, Then you could try the Restore option on Disk Utility to restore your various computer hard drives. The reason that I have not done that is that I go way back to the days of SCSI drives and old Mac OS 7 (where drives always got fired and had to be restored) and go to used to that - which is similar to what I use today - pure laziness on my part.
Using OSX 10.3.9 & 10.4.11 on a G4, G5 & Intel Macbook