There is nothing special at all about using SCCM to deploy the PolicyPak CSE. It will honor a silent install and will not require or request a reboot.

Examples of typical silent command lines to run are below:

• To install PolicyPak CSE quietly with no UI:
  msiexec /i “C:\Temp\PolicyPak Client-Side Extension x64.msi” /qn
• To install PolicyPak CSE quietly with no UI and no restart:
  msiexec /i “C:\Temp\PolicyPak Client-Side Extension x64.msi” /qn /norestart

More info on MSIEXEC command line switches can be found here:
https://docs.microsoft.com/en-us/windows/win32/msi/standard-installer-command-line-options

The only caveats are around PolicyPak Browser Router:

1. A reboot is first required for PolicyPak Browser Router to function 100%.
2. Internet Explorer should be closed when deploying the PolicyPak CSE to avoid questions of IE during installation. A script to help with that is found here.