It is currently possible to install ArcGIS Pro using command line parameters with msiexec.exe. The details can be found in the following white paper:
Unfortunately, users are required to manually configure their license manager after the ArcGIS Pro installation is complete. It would be very helpful if parameters were included in the properties of the ArcGIS Pro installation that allowed the installer to specify the location of a concurrent license manager (ESRI_LICENSE_HOST parameter, for example) and licence classification (eg. SOFTWARE_CLASS). In fact, all license settings should be configurable at the time of product installation - this is currently possible with ArcGIS Desktop command line installations. This enhancement is especially important for deployment of the software to a large organization.