I'm not sure if this was a question or a statement:

• For example, if a user is assigned to the same program twice (dynamic audience & individual) with different set of completion (due) dates, it will put the user in the exception report.

In my experience and testing, there are no exceptions for multiple assignments of users into programs. There will however be confusion on which due date the user will be assigned, and exceptions may occur if the user is given a due date from one of the assignments that causes "TIME ALLOWANCE" exception. In my testing, the priority of which due date is used is based upon the order of the assignments listed in the program assignments tab (for dynamic audiences anyway). If the user is assigned to two dynamic audience assignments, the user's due date would reflect the due date given for the lowest audience they are assigned to on the list of assigned audiences.