We were directed to PC - boarding early. It does seem that they direct you to Parrot Cay first - than as that fills to Topsiders - and probably after a little while Topsiders has filled and the early boarders who started in Parrot Cay are done, someone radios down and they start filling Parrot Cay again. Maybe sometimes they switch - but they are definately trying to control crowds.
You can eat at either location, but if they are directing to one or the other, you may find your choice more crowded (or just not ready yet).