I suspect that the installer is checking for ArcGIS v10.2 and not finding it (as you have 10.3.1), so not presenting the option for the Geoprocessing tools.
There may be a way to fool it into thinking 10.2 desktop is installed, perhaps through a setting a registry key, but I'm not sure which one.
The other thing you could try is installing on a machine with 10.2 then copying the toolbox and any supporting files from the install directory to the 10.3.1 machine.
It's probably one for support.
John