Based on some discussions here and from some outside forums I was able to create a script to perform an in place upgrade from OS X 10.11 to macOS 10.12. However, after the upgrade installs and the re-boots completes, each user has to run through the setup options. Is there a way to suppress this behavior?
You can run this script during the first boot: https://github.com/rtrouton/rtrouton_scripts/tree/master/rtrouton_scripts/disable_apple_icloud_diagnostic_and_siri_pop_ups
Create a launch daemon which will be installed before the necessary reboot. You can achieve this with this tool: https://github.com/rtrouton/First_Boot_Package_Install_Generator