We had a similar requirement for promiscuous mode and forge transmits to be enabled on all port groups when provisioned from vCD. I was given the link below which uses the vCNS API to make these changes. I'm thinking you might be able accomplish what you are needing through using the API.
http://www.virtuallyghetto.com/2013/05/how-to-enable-nested-esxi-using-vxlan.html