The content available via WSUS is the same content available via Microsoft Update. As you note, there is a distinction between WU and MU. WU is OS-only content; MU includes application content. The content from MU is acquired by WSUS by enabling one or more of those product categories in the WSUS Products & Classifications configuration options.
If this is a question of invoking the OPT-IN to Microsoft Update (vs Windows Update) on a per-system basis, so that you can invoke remote scans via Microsoft Update, that is not something that can be directly invoked by Patch Manager, but it can be enabled through a simple client-side script, which can be bundled up as a package with Patch Manager, if desired. More about the script is available from this MSDN article in the WUAgent API.
The actual script commands are as follows:
Set ServiceManager = CreateObject("Microsoft.Update.ServiceManager")
ServiceManager.ClientApplicationID = "My App"
'add the Microsoft Update Service, GUID
Set NewUpdateService = ServiceManager.AddService2("7971f918-a847-4430-9279-4a52d1efe18d",7,"")