Install MariaDB with custom my.ini file
There is no urgency of getting that setting made.  After the install is finished,


Locate my.cnf
my.cnf may have some "includes" at the end.  One of those places is the 'proper' place to do the next step.
Add any extra settings at the end of the [mysqld] section of the file.
Restart mysqld by restarting the MariaDB 'service'.


You can also set that without restarting, but the setting would be lost at the next restart:


Connect to MariaDB as 'root'.  (I like to use the mysql commandline tool, but there are other ways.)
SET GLOBAL innodb_file_per_table=0;


Now any CREATE TABLE will put the data and indexes in ibdata1.

Note:  To move a table in ibdata1 from or to its own .ibd file (tablespace), do the SET and do ALTER TABLE name ENGINE=InnoDB;