When configuring SharePoint 2007* server IRM settings in a Certification/Licensing-Only RMS model the following considerations are needed. These recommendations are supplemental to the normal steps outlined in SharePoint Intergration with AD RMS (How To).

Q: Which server do I specify in the SharePoint IRM configuration?
A: The one you want to use for protecting/licensing content.
(Typically the Licensing-only URL).

Q: Do I need to use the Activation and/or EnterprisePublishing registry overrides on the SharePoint server?
A: No.

Q: Any permission changes needed as per the documentation for standard RMS configuration?
A: You need to grant rights on the ServerCertification URL on the Licensing server. Grant permissions to the service under which SharePoint is running. That may be either the computer account if running under local system or a service account designated for the SP Central Administration site’s application pool identity.

Q: So is it possible to get the SharePoint server to certify against the root (certification cluster) and set it to use the licensing-only cluster for all the protection?
A: Yes, that is in effect what you do when you enter the licensing server URL in the SharePoint configuration.

*These steps are likely the same thing we'd need to do on SharePoint 2010, but I've not tested that scenario.