Two issues I ran into while using the new functionality of SCCM to deploy Office 365 ProPlus:
1. The setup will fail if any MSI version of Office products is installed. But the CTR setup will leave behind a registry value at HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Office\ClickToRun\Configuration\VersionToReport which SCCM uses for detection method. Hence the application deployment will be reported as successful even on failure. Unfortunately the Office Deployment Tool doesn't remove previous installations of Office and neither does this new feature SCCM.