first off, do you need to set it to that on your universal forwarders. Can't you just configure your outputs.conf to send data to all of your indexers in the cluster? I thought the site0 functionality was just for search head affinity but could be wrong.
That said, you could just deploy an app with your specific server.conf settings along with the uf install. So install install the uf, copy the app to etc/apps and restart splunk.
And depending on how many forwarders you will be managing, you may benefit from implementing the splunk deployment server. Or you could just use puppet/sccm to manage configurations similarly.
Creating an outputs.conf with just the general stanza and site flag in an app which I push from a deployer did the trick.
I am using a multi site index cluster so the outputs.conf created in a barebones install points to the index cluster master which requires site details. The process above means I can deploy a barebones forwarder to any server and update all the required settings via the app deployment process.