The natural behavior of Windows Vista and later systems is to provide a user notification when a machine is being rebooted.
The Patch Manager Update Management tools allow you to define a custom message to be displayed to the end-user following an update deployment.
The delay after installation is an item of interest, but Patch Manager easily provides you that capability as well, by setting the Update Management task to "Do Not Reboot", which will trigger the standard WUAgent notifications about a pending reboot, allowing the user to reboot when they wish. The reboot can be forced using a Patch Manager Restart/Shutdown task, or through the use of WSUS Approval Deadlines.
All in all, I suspect that you will encounter several complications trying to launch shutdown.exe within the context of the Windows Update Agent, and given that the things you are trying to accomplish are already natively supported in the OS, and via existing Patch Manager tools, I'd suggest there are better options than trying to force an execution of shutdown.exe within the confines of a package installation.
However, one option that might work .... using PackageBoot, run shutdown.exe as an asynchronous Program Task and set the "Delay before running" to be the desired delay previously mentioned. Configure a minimal delay in the actual execution of the shutdown.exe. This should allow the shutdown.exe to be spawned outside of the execution hold of the package installer. I don't know that this will actually work .. but it's likely the best option you have for being able to successfully preempt the natural behavior of the WUAgent.
You should also be cautious of what might happen as a result of pre-empting the natural behaviors of the WUAgent. For starters, you'll need to intercept the Success Pending Reboot Codes in the package definition, so the WUAgent does not get the instructions to place the machine in a pending reboot state. Failure to do that may result in the WUAgent launching the reboot despite your efforts with the shutdown.exe. Second, also be aware that since the WUAgent will be unaware of the pending reboot state, it may well try to install additional updates in a subsequent session (when it should not), and that activity could be catastrophic (if the unknown pending reboot doesn't actually happen when it should).
Personally I'd find a way to adapt the natural behaviors of WSUS, the WUA, and Patch Manager, rather than trying to force an untested/unpredictable condition onto the client using shutdown.exe within a package installation.
Beyond that.. you're in uncharted waters with this methodology ... so Good Luck! 