Hi Matthew,

The knowledge center clearly states that "you must first install a stand-alone Cognos Business Intelligence server. Then install ALM Cognos Connector to integrate your Cognos reports with your CLM server. ". So I would say it is an unsupported configuration, even though it might work fine. The possible problems you might encounter are 1. Cognos support might reject providing support, because RRDI is Rational branded product. 2. Upgrading Cognos Fixpack in RRDI tend to be difficult as it is not Cognos standalone product. 3. Configuration problem as you will overwrite Jazz namespace feature which already exists in RRDI. 

These are hypothetical, but you should be aware of these risks of unsupported configuration, if you go ahead.