MariaDB 10.2 custom install using mysql_install_db.exe
I call mysql_install_db.exe with the correct --datadir argument and root password and have all files generated. I call mysqld --remove to delete the windows service. I call mysqld --install-manual [ServiceName] --defaults-extra-file=my.ini to finally set up the service using my very own my.ini file.
When this service is started up for the first time using net start the innodb-files are created freshly in the folders defined in the my.ini file. The system database mysql uses myisam table format and had not touched the innodb files.