HeidiSQL never touched the autocommit variable, ever. But you can set it off via auto-started SQL script, in the advanced session settings.
That's right. Just remember that transactions do not work in all storage engines so try not to rely a lot on this to avoid unexpected data loss:
mysql> show engines;
+--------------------+- ... -+--------------+------+------------+
| Engine | ... | Transactions | XA | Savepoints |
+--------------------+- ... -+--------------+------+------------+
| FEDERATED | ... | NULL | NULL | NULL |
| MRG_MYISAM | ... | NO | NO | NO |
| MyISAM | ... | NO | NO | NO |
| BLACKHOLE | ... | NO | NO | NO |
| CSV | ... | NO | NO | NO |
| MEMORY | ... | NO | NO | NO |
| ARCHIVE | ... | NO | NO | NO |
| InnoDB | ... | YES | YES | YES |
| PERFORMANCE_SCHEMA | ... | NO | NO | NO |
+--------------------+- ... -+--------------+------+------------+