I deploy application A. I then deploy application B, which is higher version of the same software, packaged also as MSIX and using the same family name so both MSIX will understand they are related. I specify supersedence between them so also SCCM is aware of this relationship. If I deploy application B to the client where application A is in use, the update will not happen. It only works when application A is closed during installation of app B.
It would be great if it could be installed while the application is in use. This can be achieved with MSIX when deployed using the App Installer solution, so I thought SCCM could do this too.
We are working to improve this scenario in the upcoming version of Windows to help ConfigMgr customers easily install the app while in use so that is queued up to complete the installation after the app is shutdown.