Unfortunately there is no way of making a custom calibration. The reason why this was removed is that this is a global setting and a badly implemented calibration would affect all apps and games on the machine.
Configuration.exe is internal and may change without notice. However, it is possible to trigger a calibration from the Eyex SDK and from the upcoming new Tobii Core SDK. I will investigate if these functions can be triggered from Unity and get back here.
Stay tuned!