I didn't find anything about the three Pan Am Boeing 307 Stratoliners going in for a retrofit to Boeing after the war or even serving with Army Transport Command as C-75s. It doesn't mean they didn't, but that may explain the retention of the early B-17C wing and nacelle configuration.
Boeing's Chief Aerodynamcist Ralph Cram was killed in the March 18, 1939 crash of the prototype Boeing 307 Stratoliner.
They hired George S. Schairer to replace Cram and to develop and test the Stratoliner.
Schairer redesigned and enlarged the vertical tail section. (Schairer went on to work on the aerodynamics of the B-29, adaptation of German swept wing design, B-47, B-52, 707, XB-70, 727, 737, and 747)
The modifications, the larger vertical fin surface, and the incorporation of aerodynamically balanced control surfaces (replacing spring tabs) made its way into the new B-17E.
I think you could say that the Boeing 307's development/modification lead to the defining point between the early (Model 229 through B-17D) and late (B-17E through B-17G) B-17s.
The Smithsonian's plane was delivered to Pan Am March 22, 1940. The B-17E production started 27 September 1941.

Boeing 307 N
C19903 with the original small vertical stabilizer before its delivery to Pan Am

Pan Am Boeing S-307 Clipper Flying Cloud N
X19903 with the enlarged vertical stabilizer.

At least one of the Pan Am 307s pictured here has the "big tail".
Citations:
Abzug, Malcolm J. and Larrabee, E. Eugene, Airplane Stability and Control; A History of the Technologies That Made Aviation Possible; Second Edition, Cambridge Aerospace Series, 2002.
Schairer, George S. "Directional Stability and Vertical Surface Stalling", Journal of the Aeronautical Sciences, Vol.8 No.7.
http://www.air-and-space.com/Boeing%20307%20N19903.htmhttp://www.historyofwar.org/articles/weapons_B-17E.html