@pueo the installers cache and then attempt to install once they are fully downloaded. The expected behaviour of what happens if the app is running to this point has been dependent on how the installer was constructed by the original software vendor. We were trying to use the original vendor packages as much as possible and were only repackaging if the original installers were either not available in a .pkg format and/or were not available as a universal installer. I provide a little more information about this here https://www.jamf.com/blog/jamf-app-installers-faq/
Unfortunately many vendor installer packages have some 'quirks' when they are deployed via the InstallEnterpriseApplication MDM command versus standard GUI or CLI methods. This will require us to repackage more titles than originally estimated to address these issues though this should provide a more consistent user experience.