Last week the 1806 update for Configuration Manager current branch was released.
Among other functionality, MSIX support has been added to the 1806 update for Configuration Manager current branch.
You can add a MSIX package just like you would do with any other application.
Once created, you can add the package to the Distribution Points and start deploying it to your clients.
Want to know more about what's new in 1806? Have a look at https://docs.microsoft.com/en-us/sccm/core/plan-design/changes/whats-new-in-version-1806
Ingmar Oosterhoff, Johannes Freundorfer and Matthias Herfurth