If wanting to ensure the users can continue to work uninterrupted by a black screen (a result of Windows Explorer restarting in the installing user’s context), a registry setting needs to be created before installation. You may need to execute the installation commands as sysnative to force the registry key to appear in the correct spot, and still have a single application in Intune. You may also want to setup a restart grace period so that the machine will not automatically restart after installation. Below screenshots may help further:
REG ADD "HKLM\Software\South River Technologies\WebDrive" /t REG_SZ /v "NextGenUpgraded" /d "1" /f
msiexec /i "WebDrive+Setup.msi" /qn WRAPPED_ARGUMENTS="/S"