From my reading of Walt's material the reason the shallow with brood is moved down is to artificially stretch the broodnest downward for pollen storage. After the brood is hatched, the workers start storing pollen in the bottom super, using the natural break between shallow and deep as break between pollen storage and nursery. It is not to make more room overhead for laying, as it would be the case in reversing deeps, since reversal dedicates bee energy toward moving stores around.
The shallow that is moved below deep should be heavily populated by capped brood, so moving capped honey to the supers above should not be consequence of that reversal.
One does not have to reverse deep and shallow, this is simply done to enable pollen storage in a separate box, rather than bottom of a deep. This way the deep is wholly dedicated to raising brood, and bottom box is dedicated to pollen and bee bread making.