Is it possible to use SSL when connecting to Google Cloud SQL?
When using my Navicat client I need to configure certificates - so I have no idea how that would work with DF?
DreamFactory does not have settings for secure vs insecure sql connections. What most people have done who have a need for this type of connection is to create a persistent secure tunnel between the machine hosting DreamFactory and the destination database server. Then you can add it to your dreamfactory as a service as localhost with the appropriate port number for the tunnel connection.
Is it possible to have a script run (prior to the DF service attempting to connect to the MySQL DB) that would setup the tunnel and provide the local port number back to the service?
No such functionality exists within DreamFactory. This is more a question of configuring your infrastructure. I would look into autossh and cron to start and maintain the connection. Then it will always be available to DF.