Looking at the letter of 314.28 and 376.23, it seems clear to me that the inspector is technically correct, unless you want to argue that the wireway is not being used as a pull box, because the conductors get pushed from the wireway into the enclosures just above. [Also, the difference between the 4" required by 376.23(A) for deflection of 3/0 conductors, and the 20" required by 376.23(B) seems oddly large.]
So I would like to understand why from a practical point of view this requirement is unreasonable. If the conduits exiting the top of the wireway were 10' long instead of a few inches (move the panelboards up a story), would the 20" requirement now seem reasonable? If so, what aspect of having the enclosures just a few inches above the wireway makes the difference?
Perhaps 314.28 needs an exception for pull boxes located sufficiently close to the equipment in which the conductors are terminated.
Cheers, Wayne