The B-29A used a different form of wing center section construction. The B-29A was built by Boeing at the Navy-owned Renton plant. While the B-29s were built in other factories. On the B-29 the wing center section was split on the centerline and bolted together. This center section held the engine nacelles and the outer wings were attached to it. On the B-29A a very short one piece center section went through the fuselage and did not project past the sides of the fuselage. sections of wing holding the engines in pairs were attached to the center section and the outer wings attached at exactly the same points as the B-29.
Apparently (but I could be wrong) this change in construction left less room. I have no idea why this one factory used this form of construction unless it was to use some legacy tooling from the Boeing Sea Ranger flying boat which was to have been produced by this specially built factory.
The wing was about 2 feet shorter than a B=29 wing and they used a similar or perhaps identical airfoil.
Just a wild guess.