In Windows, most applications install by running an MSI (Microsoft Installer) compatible app/file.
MSI's contain a great deal of often complex installation logic, settings, configuration mechanisms, etc. While you can unpick an MSI, modify it and repackage it to your liking, this can result in badly broken app configurations.
Different apps configure themselves in different ways - some use the registry, some use XML config files, others use config files with their own format. Some use multiple config points - registry, files, etc.
If you really want to configure this app, I recommend trying to work out where it keeps all its config data. Then you can write the necessary script to allow you to modify the registry and/or modify the app's config file(s) with the settings you want.
Understand, however, that unless you're careful, there's a good chance you could confuse the app - often in subtle, hard-to-track-down ways and you may end up corrupting data (particularly if the app stores data in files and/or databases)!