Well, after a bit of research on this, I found that my understanding of the CLI output format of set was a bit flawed. Downloading the configuration from the Palo Alto via the standard commands of "show config running" or "show config candidate" within the non-config mode is a valid way of getting the same information that is in the method I described above, however, you do not get the same format. The "set" method will give you commands you can cut and paste into the Palo Alto directly. The "show config" method will give you the XML output of the configuration file. The later is a little less friendly if you want to copy paste into a CLI.
Regardless, the problem I have is still a problem. I want to be able to get the "set" commands from a config backup.
On a side note, we are using Palo Alto Panorama on our FW deployments. We can backup the config for Panorama as if it were another fw tied to NCM. This allows us to capture anything pushed out via templates or policies.