I think Manual J looks at a static scenerio and doesn't fully take stack effect, reverse stack effect and convection into account. In my experience in my home at least, even with a assymetrical 1500 up/1700 down floor plan and higher ceiling downstairs, during normal occupancy and not cooking in the kitchen, upstairs cooling is about 60/40, and in winter heating is about 70/30 including partially heating a full unfinished basement.

Therefore airflow varies dramatically all season.