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This functionality has been added to version 2018.1 due out in the next week or so. Any previous version only has this support for patches in the agent setting.
Aside from that, it "doesn't care" about which kind of executable (EXE, MSI, etc) is being run.
It just checks whether a given process (i.e. PowerPoint) is running in fullscreen mode, and - if so - won't perform stuff.
Whether the file behind the operation is an EXE or an MSI or whatnot, that matters less to not at all.