MySQL: Can't find .ibd files after turning on innodb_file_per_table
The .ibd files will be under the innodb_data_home_dir under a subdirectory, the subdirectory name matching the database name.

Given innodb_data_home_dir=/etc/local/mysql/data and innodb_file_per_table is set:

 SHOW VARIABLES LIKE 'innodb_data_home_dir'
 SHOW VARIABLES LIKE 'innodb_file_per_table'


then when table test.mytable is created, the .ibd file will be located in /etc/local/mysql/data/test/mytable.ibd 

(It's possible that the ibdata1 file will grow to accommodate rollback for transactions. When a transaction is run, pre-change copies of blocks get recorded, in case you issue a ROLLBACK, and also for the benefit of concurrent transactions (with an appropriate isolation levels), that need to reference only committed changes, and not any uncommitted changes.)