Ok, so here's the deal. I created a new management group. I attempted to add the second AD domain to this second management group and recieved an error:
The scope is already assigned to Management Group (NAMEOFNEWGROUP). You must delete the scopes current Management Group assignment before attempting to assign to another Management Group.
DataPortal_Insert method call failed
DataPortal.Update failed
Apparently it's still seeing that identical NETBIOS name for the domain and preventing me from adding the domain to the second mgmt group.
That really sounded like it would work however after trying this I'm still coming back to there being an issue with the database not allowing this.