There may be more to it than this, but one reason for this is visible in the XML code for firewall rules - the objectID is that of the ID listed in the Managed Object Browser. The objectIDs vm-25 in vCenter1 can reference a different VM than what objectID vm-25 may reference in vCenter2. I suspect this is the rationalle for the 1:1 relationship.
I would view the 1:1 relationship as more of a design requirement rather than a limitation as. NSX 6.2 bring to the table the Cross-vCenter deployment topology. This allows you to bring together multiple vCenter/NSX Manager instances to be managed centrally. The cross-vCenter design allows for one primary NSX manager and up to seven secondary NSX managers, each tied to their own vCenter.
