I believe before the arrival of the Superliner IIs in real life, the old Hi Level transition cars were used and that is what is being modeled, so it is prototypical for early trains.
This is correct. Several El Capitan cars were upgraded to HEP and run with Superliners prior to the introduction of the Superliner II cars. This included coaches, lounge cars, diners, and coaches that were converted to coach / dorm transition cars. The single level El Capitan dorm with the streamlined roof profile that matched the Budd El Cap cars was retired with the introduction of the Superliner fleet.
Former El Cap coach / dorms had a few configurations. One, which GGD is offering had the crew beds on the lower level of the car. The other configuration utilized the front half of the transition coach as the dormitory space, while the rear half of the upper level had coach seats.
When I rode the Southwest Chief in the late 80's and early 90's the train always had a former El Cap transition dorm behind the baggage car and ocassionally had former El Cap coach, lounge, or diner in the mix with the Superliner I cars.