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If you launch the Atlas.ti 5 exe installer, and allow it to go through to the point where you start to input information, you can actually grab their MSI from C:\Windows\Atlas.ti Downloaded Websetup. Then you can use your application of choice to modify this package however you'd like, and deploy it via your preferred method (mine is GPO).
Also, the properties you may need to modify in the property manager for your licese are ISX_SERIALNUM and ISX_SERIALNUM_EXT. These properties do not show up until you look in direct editor. So, add them to the property manager. The first part of the license goes in the former variable you create, and the last part in the second variable.
Run setup.exe /r and install the app, grab your recorded install file: c:\windows\setup.iss and dump in the application file dir on your server, install using setup.exe /r for a silent automated install.