Your understanding is absolutely correct ... the product is exceptionally well suited for deploying software ... I did not mean to imply that it wasn't.
However, what is critical to understand is where the boundaries exist between what is Patch Manager operations, what is WSUS operations, what is WUAgent operations, and where the sole functionality of the *application* begins. To that point, once the WUAgent launches the installer, it's ALL the application. If the application fails to behave as expected during the installation, there's nothing you can do with SPM/WSUS/WUA to fix that -- unless, as I've suggested, the behavior can be modified via the installer's command line parameters.
Alternatively, you can also script the creation of the desktop, taskbar, or Start Menu icons via a VBS script that can be executed as a <postinstall> task using PackageBoot if the installer provides no methodology for doing that otherwise.