As documented here, setting a dokku superuser actually results in preventing apps from being deleted via the command line, which is a side-effect that likely comes quite unexpected to most users.
Despite the helpful warning message
It appears that you're running this command from the command line. The "dokku-acl" plugin disables this by default for safety. Please check the "dokku-acl" documentation for how to enable command line usage.
it took me some time to figure out what was going on.
Once the relevant feature has been deprecated for long enough, I suggest to move to DOKKU_ACL_ALLOW_COMMAND_LINE=1 as the default.