Windows Installer has built-in features to allow you to customize the install via PUBLIC properties (uppercase) set at the command line or applied via a transform (Windows Installer's mechanism to apply substantial changes to the vendor file - it is a partial database that gets applied to the installation database from the vendor at runtime). If that doesn't work you can try setup.exe /x or setup.exe /extract as well. Then you are dealing with an MSI file wrapped in a setup.exe. Try to run setup.exe /a from the command line and see if you get an option to extract files to a "network install point" (administrative install). If the setup is an MSI the same team can also modify that for you according to your specifications.
If you are in a large company there might be a team dedicated to packaging software like the one you mention. It is generally done in large corporations for very large software distributions. This is a specialist task requiring good understanding of Windows and setups. You should be aware that for legacy style installers a common practice for large scale deployment is to capture the legacy install with an application repackager tool, and then compile an MSI file to use for installation (effectively converting an installer from an old format to modern MSI format). An MSI database can also be wrapped in a setup.exe. Essentially the installer is either a Windows Installer database (MSI) or something else - generally a setup.exe of some kind. I had a quick look for that installer, but didn't find it easily.
I haven't really tested it much, but it is from Heath Stewart - Microsoft Senior Software Engineer ( github). UPDATE: See Windows Installer PowerShell Module on (scroll down for description, use releases tab for download). UPDATE: Several links towards the bottom with information on how to handle installation, configuration and file extraction for setup.exe files.
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