Server loses a part of configuration and some plugins are not activated due to pre-installed mysql-common

Modern Debians/Ubuntus, e.g. Stretch or Bionic, have MySQL's mysql-common installed either right from the start with the system installation, or fairly quickly with some commonly used packages as a dependency:

ii  mysql-common                          5.8+1.0.4                         all          MySQL database common files, e.g. /etc/mysql/my.cnf

It installs my.cnf:

drwxr-xr-x 2 root root 4096 May 15  2018 conf.d

lrwxrwxrwx 1 root root   24 May 15  2018 my.cnf -> /etc/alternatives/my.cnf

-rw-r--r-- 1 root root  839 Aug  3  2016 my.cnf.fallback

The config is empty, it only includes conf.d:

!includedir /etc/mysql/conf.d/

When MariaDB (of any existing version) is installed, it doesn't override existing my.cnf, so whatever legacy stuff MariaDB usually has in it, doesn't get activated. It is not a big problem. However, it also means that the cnf file doesn't include mariadb.cnf, and thus doesn't include mariadb.conf.d, where some of separately packaged plugins install their config files. So, for example, when mariadb-plugin-cracklib-password-check or mariadb-plugin-rocksdb are installed, they don't get activated.