Yes, it is a correct behaviour. If you change default values, you change them only for NEW models or NEW objects. If you e.g. change a default value for an entity, the new default value will be used only for new entities, not for already existing ones.
Concerning the settings in DDL Script Generation dialog, the new default value will be used for new models. To change the settings in existing model, feel free to define them and then simply click the ‘Save Settings’ button.
Generally, it stands that settings for script generation are saved within a model. So, TDM3 allows you to define particular script generation settings for each model.