there are time when you may need to. most often, you will be able to rearrange a few frames to accomplish what you need to do. if the bees are following the script, they will have made the brood nest in the middle of your box configuration. they will fill in honey over the top of the brood. as they do this, they move down. that's why you put the honey supers on the top.
so...if they are doing what they are supposed to do, what happens when you swap the boxes? you break the brood nest, put whatever honey there is on in the middle of the brood nest so that the queen may not cross it either up or down (depending on where she is). at the least, you will disrupt whatever they are doing because they got busy way before you got a chance to get in there and check.
because you are confining them in a space youhave chose, you may need to adjust frames from time to time. if there is to much honey, you may need to remove some and expand the brood nest. if they really won't move up or down, you may need to move a frame of brood up or down to attract them. lots of this stuff takes some experience to evaluate, but with bees i have found that it's better to do nothing than to "help" when i'm not sure.
why do the books say swap boxes? because that's what's always been done so we keep doing it.....and because on occasion you might need to....but IMHO, not often.