In a prior post, How to Customize Office with the Office 365 Click to Run Deployment Tools, I covered a few basics of customizing an Office 365 Click to Run install beyond what is supported in the standard configuration.xml file by using a simple Batch (.bat) file. Since Intune doesn’t support processing Batch files or VBS files, today I’m covering how to compile your scripts and batch files into a self contained executable.
There are hundreds of tools out there to compile executable, but we’re going to use the one Microsoft provided along with Windows, the Iexpress Wizard.
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Run iexpress.exe as an Administrator

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Use the default of “Create new Self Extraction Directive file.”

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Use the default of “Extract files and run an installation command”

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Name your project.

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Select if you want to provide a prompt.

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Provide a license prompt if desired.

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Add the customized batch file, setup.exe and the customized configuration.xml file. If other files are included, make sure they all have a unique files.

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Select the custom batch file for the installation command. Make sure to add the cmd.exe /c as below.

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Select the focus of the app, in this case we will be using Hidden.

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Provide a finished message if desired.

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Provide a path to save the executable. I’ve run into odd scenarios when saving outside of the work folder where the other files reside, as such I recommend saving the executable in the same folder and not using any spaces.

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Configure if a restart is desired.

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Save your Self Extraction Directive

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Click next to create the package.

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Done!

You now have a single .exe that can be run without parameters and can be delivered via Intune.