1- You can SSH on a GAE Flex instance for debugging purposes by going to your Console > App Engine > Instances > Select SSH on the selected instance.
2- Since the last possible solution offered is not feasible for you, can you detail why would you want to "createsuperuser" on the first place. If your intention is to create a "power user", you can create a root level user on your DB like
this StackOverflow thread. If you want a "grant all" permission, this will not work because Cloud SQL does not support "super" privileges as documented
here.
3- In addition to #2, provide the versions of your Django, Cloud SQL, and Google Cloud SDK.