How can we configure the 10.3.1 NCM Self Certification to grab the entire configuration?
The NCM Self Certification tool kit is almost identical to an SSH session to the device.
Any command you would normally enter into a SSH session would have to be entered into the command list.
For Cisco, for example, you would have to set the terminal length to 0 to see the entire configuration.
For other vendors or operating systems we advise you reach out the the vendor or vendor community to get other commands to display the entire configuration as not all operating systems support "terminal length 0", even other Cisco devices like the WLCs and ASA Firewalls.
The following URL has a bunch of different examples for Cisco devices.
Other vendors, such as Juniper, should have a similar document. If they cannot be found via searching contacting the vendor is the best option.