I had a chat with Microsoft about that issue also.
I will be able to execute the setup.exe with a command line parameter and update windows 8 to 8.1 IF you have the enterprise version installed.
If you use any other windows version, at Microsoft told me, you will either manual update through windows store or reinstall the operating system on the client.
Very unsatisfing answer, that Microsoft changed this behavior in Windows 8...
Regards
Fabian