from http://www.scconfigmgr.com/2018/09/24/deploy-win32-applications-with-microsoft-intune/

WIN32 APPLICATION DEPLOYMENTS

The ability to “package” applications for deployment in Microsoft Intune is something that has been highly requested by many organisations making the move to management of devices through Intune. Although there is a fundamental difference in deploying applications through Configuration Manager and Intune, Microsoft is developing tools to provide similar functionality across the management stack. Up until now it it has been possible to deploy applications through Intune, this relied on a single MSI installation file with no external dependencies. In some cases this meant that repackaging of applications was the only method of deploying those business applications, thus being a time consuming process.

Today it is now possible to deploy applications through Intune without those restrictions, this process creates a packaged container of the setup files along with command line installation and uninstall commands.

This is a significant feature towards bringing Intune from the realms of “good for mobile device management only” to “also good for desktop management”.

SCCM currently does (and probably will for quite a while) have additional functionality which larger enterprises require – however, this is a good step in allowing smaller organisations more flexibility in their deployment options.

Note: as of 25/9, this feature is available with an Intune tenant running a preview of the GA release.