I am far from an expert, however I can tell you what little I know.
Lexia has an IRC rating which was required to enter the OSTAR (2009 and 2013) and the AZAB (2011).
Fortunately a Sunbird 32 junk rigged schooner had been registered for IRC previously and so it was just a matter of providing details of any changes, eg a feathering prop when fitted. (I would imagine that it might be more difficult to start from scratch with a model that had never previously been IRC rated.)
According to the IRC, Lexia is getting slower with age - just like her owner! Indeed the AZAB gave me a trophy, apparently for going slowly, rather like a slow bicycle race.
As regards sail area - the sail area is the sail area of the junk rig sails as per the sail plan. And the junk rig is rated or entered as being without spinnaker.
The only possible point of contention was that IRC insisted on recording the junk rig as a "Cat Ketch", presumably because that was the nearest description in the list on their computer system. I didn't bother to argue.
On the few dealings that I had with the IRC Rating Office they were very helpful.