Below is explanation of the MySQL specific preferences available in Database Workbench:
Option
Description
Query timeout
Specifies the number of seconds that the SQL Editor will use as the default query timeout.
Default storage engine
When creating a new database, or when editing the database options for the first time, the given storage engine will be used as a default for all tables. This can be overridden in the database options in the Enterprise Manager and when creating the table.
Default isolation
The default transaction isolation used in the SQL/Script Editor.