The secondary server was actually to provide two very important things for the network. Primary server would be the connect to the labs. This would give the fastest connection to the labs directly from the hard drives. The Secondary server would have a backup copy of the software, and in the event of any type of failure on the primary server, logins could be changed. The secondary server being setup in the same TREE as the primary allows for a easy way of switching configurations. Being in the same TREE also allows for having a replica of the NDS directory services. Novell actually recommends having atleast two replicas of the NDS of a Tree for this protection.
In the current configuration, all servers are in seperate trees, with no NDS replication, but they are not real networks.