Competitors to WCA allow you to add multiple tags (or flags) to the contact. Example - when a contact enters a program - add a tag - when they exit the program add another - or in the program have a step to remove specific tags. This way you could create a query for another program using the rule "does not contain... tags." This way you can now use the query in another program without causing issues on the back end (the reason why you can'tuse a query that queries another query - Ha).