This is more a question for e.g. the LinkedIn “SDTM experts” forum (LinkedIn Login, Sign in | LinkedIn) or the LinkedIn Define-xml forum (LinkedIn Login, Sign in | LinkedIn)
It has nothing to do with Pinnacle21 …
But ok …
Essentially define.xml is about what is planned to be done. That is why we also always recommend to generate a (prototype) define.xml even when do data is available yet.
IMO it is bad practice to generate the define.xml at the end of the study, based on the collected data.
Whether you add ValueLists is your choice: there is no obligation at all except for the SUPPxx datasets. As long as you document everything very well, taking care that everything is clear for the reviewer, all is fine.
Remember that you can always use @def:CommentOID, pointing to a def:CommentDef on several elements, to add comments.