Hi Kevin
In our case we have configured the CRM and BI systems for direct role assignment only then the administrators have to periodically manually clean up the direct role assignments and move them to the position. Good thing was that we were already on position based security and changes are minimal so not a big job to administer. Other consideration was to have a hybrid solution with CUA and assign all roles within the central system. However this would add an additional layer of maintenance as all roles from child systems would need to be associated with a composite role within the central system.
Regards Bill