The mysql_secure_installation script has some options, that should be explained in the man page.
This script is used often to make admin sure, he doesn't forgot to apply some essential security settings, before opening server to the public.
Some information about the options can be found here:
I filed this issue in order to solve https://bugzilla.redhat.com/show_bug.cgi?id=1260821.
The --defaults-file option, for example, is quite essential, when you customize your server configuration and atleast that one should be added.