Why does MariaDB 10.1.16 vanilla installation comes with an almost empty config file? Why does MariaDB 10.1.16 vanilla installation comes with an almost empty config file (/etc/my.cnf) ? Whereas it is not the case for MySQL. The config file for MySQL is usually not empty.
Not sure if it answers your question, but in /etc/my.cnf:

#
# include all files from the config directory
#
!includedir /etc/my.cnf.d


One of the files in this directory is: 

mariadb-server.cnf


This file and possibly other files as well does not exists in MySQL.