This seems like a flaw in the system. When editing end users, the system provides the ability to put the end users into several groups (which is what we need). The active directory pull group assigns the end user's to a department. We were adding staff to the additional handmade groups for special purposes.
For example; I was creating management groups (Directors and Deputy Directors) as when they put in a ticket, they should be processed in an expedited fashion compared to a regular end user's ticket. The only way I can see to do this is to assign the directors to a handmade group and use the routing conditions to change the priority of the ticket. I can't take the directors out of the Active Directory Groups because the department they are in may determine which technician gets assigned to the ticket. Also, I can't take the directors out of the Support Central AD groups without taking all the users out of Support Central AD groups.
The Active Directory group only provides for routing via the Active Directory department attribute. There are several examples I could provide where a client (such as us) would want to route tickets based on other criteria then just the department. We don't want to go with strictly handmade groups as that would be a pain to maintain as in most instances, the department attribute is sufficient for routing most of our users tickets.
If (in the future) the Boss Central Support could route tickets based on Active Directory Groups (so we don't need to recreate/maintain equivalent Central Support handmade groups) that would be great because it would save us time on maintenance and prevent things from getting out of sync.
In the meantime, we can deal with Support Central pulling the departments out of active directory and us having to maintain some Boss Central Support handmade groups provided end users can be in both types of groups concurrently.