This issue is a result of further investigation of JBIDE-19431 and JBIDE-19535. This investigation showed me that the generation of DDL works fine (wether a defined console configuration is used or not) unless version 4.0 of Hibernate is used.
So for JPA 2.0 (which uses Hibernate 4.0 under the covers) the DDL generation does not work if the console configuration is used, nor when the use of a console configuration is disabled and Hibernate 4.0 is selected in the DDL generation dialog. It works however for Hibernate 3.5, 3.6 and 4.3.
For a JPA 1.0 project, DDL generation works with the console configuration and when console configuration is disabled and Hibernate 3.5, 3.6 or 4.3 are selected in the DDL generation dialog.
For JPA 2.1, only Hibernate 4.3 is a compatible Hibernate version and DDL generation works in this case both with and without using the console configuration.