If you set the deployment template to use both a Pre-deployment reboot and set the deployment action of 'Shut down SQL Server' it will follow this order of operations:
1- Performs reboot
2- When system starts back up it will run the command to shut down SQL server.
This can be seen if you look in C:\Windows\Propatches\Install on the target system. There are actually two different batch files created - the first batch file that is run is just to perform the pre-deployment reboot. Then the second batch file is run when the system is booted back up, and this batch file contains the command to shut down SQL server as well as the commands to run patches and the post-install reboot.