I create a cmd file with for example this command: msiexec /i "AcroRead.msi" TRANSFORMS=" AcroRead.mst" /qn /L*v c:\InstallAcrobatReader.log and create an *.intunewin file with the IntuneWinApputil.
When publishing the app in Intune type the created cmd file as install command and it works like a charme...;)