Setup Assistant is looking for a seed router on each port configured for AppleTalk. The server (a single host) cannot be present twice on the same network (configuring multiple ports for AppleTalk on the same network). So, it is polling for a seed router that would confirm that the server is on a routed network. The server can have multiple ports using Appletalk if each is in a different zone.
If the Setup Assistant does not find a seed router, it prompts you to set one up. If you are running the Setup Assistant before connecting your Ethernet cables, you should connect them at this point to get a correct configuration.