Thank you very much for the attention you pay to the forum and Toad Data Modeler Team wishes you and all the other active forum members and TDM users a happy new year and success in business activities!
Re your suggestion: There might be various ways how to get what you need and having the Generate option for each workspace might be one of them. Unfortunately there are objects like procedures, functions etc. that cannot be added to a workspace and in future you might need something similar for such objects as well.
Now I can recommend you to select workspace on DDL script generation dialog and then manually check or uncheck checkboxes on tab entities, procedures etc…
If you wish to get more, I think Categories could be used in combination with scripting. You are experienced user of TDM and I suppose you already explored the power of scripting. In the following article I tried to explain how to use categories via scripting:
Imagine how easy it could be to write a macro that would allow you to select entities and add them to “Copied” category (objects in such category should not be generated), a macro that would set Generate option to false for all objects that belong to the “Copied” category… a macro that will reset the state of Generate option and so on… With a small set of simple scripts you can get better tool that does not offer plenty of settings for rarely used scenarios but helps you to achieve desired results easier.