As detailed in this blog post PDQ Deploy Pro has some architectural differences with prior versions.

This new version no longer requires SQL Server which significantly simplifies the installation and maintenance but does result in the loss of real time sharing of installers.  This is a capability we will add back in the future in a way that doesn't require the complexity of a new database server to install and manage.  Installers can still be shared by using the Import/Export functionality in the console.

As for the installation process the new installer doesn't "install over" all of version 1.2 as normal. This is because version 1.3 combines all components into a single installer while version 1.2 had the components installed separately.  Once the installation is complete and you are ready you will need to uninstall the old console and SQL Server Express (if you installed as part of PDQ Deploy Pro.)  These components may be on different computers.