You can now set a limited number of flags on your instance, see this Google doc.
Unfortunately this does not include the interactive_timeout flag.
Original Answer
It is not possible to set global variables on Cloud SQL with either the Cloud Console or gcloud utility.
And Cloud SQL does not support granting SUPER privileges see the bottom of this page .
However in this similar question Google Cloud SQL max-allowed-packet a Googler has answered saying that you can email them at cloud-sql@google.com with the project and instance name and they can configure that settings for you, so they may be able to set interactive_timeout for you.