I think it's that once you flip it upside down and start scrunching, it works the conditioner and/or product more evenly all through your hair. If you're standing upright, you may not get it all underneath - most of it may just wind up on top of the canopy.
I rake it all through too, top first, then flip my head over and do more underneath with the scrunching technique. This way you get all parts of your hair, which, if your hair is thick, you don't want to miss any sections.