The main difference between these two extensions is what they would be used for. When you say.Exe, this means that the file that you are trying to open is an executable file. This can be the file of a program. When you say MSI, this means that the file that you are trying to open is part of the windows installer. One thing that you should know is that even MSI files are also likely to have .exe files too in order to work.
You want to make sure that the installation of the programs that you would choose will be properly managed otherwise you might make some mistakes that will cause the programs to not run smoothly.
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