I agree; I can only assume it's less of an overhead for BA to calculate the miles and TPs that would be earned for flights between any two points in the USA rather than maintaining an up-to-date list of all direct point-to-points operated by AA, returning an error when no such direct service can be found.
It does state on the mileage/points earning calculator:
Originally Posted by BA
Enter your trip according to the flights shown on your itinerary. For example for Edinburgh to JFK via London, enter Edinburgh to London then London to JFK.