Below is explanation of the MySQL specific preferences available in Database Workbench:
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.
The default transaction isolation used in the SQL/Script Editor.