How can I get the MySQL super_read_only setting to work?
This seems to be a consequence of MySQL Bug#79328.  I'm assuming you started MySQL Server with either command-line or configuration file options to enable --super_read_only mode.  Because of the referenced bug, the --super_read_only option is not properly processed at server startup.  Until this is fixed (hopefully soon!), --super_read_only must to be set dynamically.