Scenario
During installation of Configuration Manager 2012 RC2 the prerequisite checker lists a warning for the prerequisite: Verify site server permissions to publish to Active Directory although the required permissions are in place.
As the environment might expand and more site servers could be implemented it was opted to grant the permissions using a domain local security group which has the site server computer account added as a member.
Troubleshooting
First check was to verify if the required permissions on the System Management container are implemented for the group. Additionally it was confirmed the site server computer object was added as a member. When running the prerequisite checker it still shows the warning even though permissions are in place.
In a second scenario permissions were implemented on the System Management container using the computer object instead of using groups. When re-running the prerequisite checker it did no longer show the warning and passed the check.
Resolution
According to feedback received this is behaviour as expected.
This was logged earlier as a bug for the RC1 release of Configuration Manager 2012. The bug report mentioned this would be fixed as of build 7688. Apparently at that point the fix was to reword the explanation offered by the prerequisite checker as opposed to implementing a fix that would have to create a dummy object in AD to test actual permissions.
Bottom line: the warning message can safely be ignored as long as the permissions for the group containing the site server(s) are correctly implemented.
