Hi,

In the default server.cnf file that gets shipped with the yum package, there is a [mariadb-10.1] section.

I like this example, but maybe it belongs in a /etc/my.cnf.d/example-multiversion.cnf file?
In any case, please update the default server.cnf to something where appending new configuration parameters always work. If you don't agree it should be in a separate example file please at least put [maridab] or [mysqld] as the last section.