Du kannst, wenn das MySQL Handbuch nicht lügt, die Tabelle aus dem Shared Space herausspalten:
Da steht:
To move a table from the system tablespace to its own tablespace, change the innodb_file_per_table setting and rebuild the table:
SET GLOBAL innodb_file_per_table=1;
ALTER TABLE table_name ENGINE=InnoDB;
Tables added to the system tablespace using CREATE TABLE ... TABLESPACE or ALTER TABLE ... TABLESPACE syntax are not affected by the innodb_file_per_table setting. To move these tables from the system tablespace to a file-per-table tablespace, they must be moved explicitly using ALTER TABLE ... TABLESPACE syntax.