Running multiple DNS Seeds
Asking this question on Super User might have resulted in a quicker and more response as this is strictly speaking not limited to Bitcoin.

Sipa's bitcoin-seeder allows you to run the DNS node on a port other than 53, so that you could set up a DNS seed for each of the networks you want to support. In order to receive incoming queries and respond to them you'd then set up a BIND server that acts as a slave for the individual subdomains and then delegate incoming queries to the corresponding bitcoin-seeder. The zone configuration of the BIND daemon does allow you to specify ports other than port 53.