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You should read documentation to get knowledge of isolation modes and how they can affect access to computer resources.
MSI packages are for installation purpose - notebook usage of application. EXE files (or DAT files when package is greater) is for application streaming. It depends what you want to do. I prefer application streaming when I implement linked clones, because as you said, application would get installed all over when clone is refreshed.
***Good question is half of the answer...***