Just posting this here for anyone facing this problem.
Deploying the msi with “/qn” command-line options as a packaged Win32 app in Intune did not work. Explorer would close and not re-open again, installation would fail.
Deploying with the PowerShell script above as a packaged Win32 app would install but Explorer would close and not re-open.
The only workaround is the deploy the PowerShell script as a packaged Win32 app and change the device restart behaviour option to ‘Intune will force a mandatory device restart’. Explorer closes then soon after the machine should reboot with the app successfully installed.