Sonal,
You can query CDO's when scoring if that's what you are asking, it is done in the engagement filtering. What do you mean using a different filter for scoring? Anyone that satisfies a criteria that is queried in the model will receive a score irrespective of whether they are know or not ie email address. Once they are known, the score will be added retrospectively. If this doesn't help with your query, please provide a little more clarification and I will try and help.
Tim