My SWAG would be that it does not include the rub rail because that data would be generated by the naval architect and the rails added in production. Also, measurement w/o rails would be more useful in generating performance data. But I'd be interested in hearing from someone who knows. The rub rails can't add much more than 3". Do you have a situation where that is critical?
The aluminum rub rail on the 38 only adds maybe half an inch total. It covers the deck/hull flange, which is part of the boat. I don't see how the flange could be ignored in stating the beam. But who knows?