The problem is pretty simple.
When you use "mysql_secure_installation" script, it will ingore all of yours current configuration.


However, there are some options, that can be used. One of them is used to add your custom config file. It is documented, for example, here: [2]
Unfortunatelly, the "man mysql_secure_installation" is quite short of infromation. (same as [3])


I believe, the information about options really should be added to both manpage and [3].
That should also solve the bug, without any 

[1] https://bugzilla.redhat.com/show_bug.cgi?id=1260821
[2] https://dev.mysql.com/doc/refman/5.7/en/mysql-secure-installation.html
[3] https://mariadb.com/kb/en/mariadb/mysql_secure_installation/ 

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I would like your general opinion about this.
Based on it, I can file issue on JIRA.