“Seems I recall the NKP had some auto cars that were built based on an earlier design, where it was found the new diagonal pressing interfered with the loaders, and so the cars were built with diagonal panels EXCEPT for two; those were the older rectangular design to gibe the needed clearance.“

Dennis, 

The "mixed panel" roofs were discussed some time ago: 

I have confirmed the following cars having the combination diagonal
panel/Murphy panel roofs. There were probably more. All were auto cars
with 15' wide door openings built new with these roofs. You have
already referenced Tony's book and some specific SP cars.

D&TS 5000-5099, 2-55, Greenville
MP 88900-88999, 6-57, MP
NJI&I 3300-3399, 1-51, ACF
NKP 86100-86249, 12-49, ACF
NKP 86200-86349, 1-55, Greenville
Numerous SP cars, 1950-1956, all built by SP
WAB 19800-19999, 5-53, ACF
WAB 20000-20199,"

Guy Wilber wrote:

"Ed,

Other than the SP cars, none of the above cars were equipped with Auto~Loaders. The balance were in parts service.

Whether, or not, the cars were purchased by the respective roads contemplating installation of Auto~Loaders I do not know. Until Evans developed the Type "F" with a boom hoist and the Type "G" the rectangular panel was required to facilitate the supports for the lifting sheave hanger frame and the similar frame that supported the safety hook assembly used to secure the racks when stored against the roof of cars.

Evidently, Evans lift assemblies were also used within auto parts cars utilized for shipping car bodies. I have some literature on the system but have yet to find a complete installation drawing. I believe that may offer another connection to the mixed panel roofs."