Not putting the jiggle valve at the top would hinder the air getting out when you refill, and may even mean some air is trapped in the thermo housing.
Although the book says the system is supposed to hold
14 liters, with my car (3SGE) I can only ever drain out about
9 liters.
I assume the overflow bottle may hold a couple of liters, and that would be included in the 14 liters capacity.
Also in my motor, I have no block drain tap, so some coolant would stay in the block.
BTW,
raising the rear with car ramps is great if you want to change a thermostat, because you then only have to drain out about 2-3 liters from the radiator tap and catch it in a plastic dish.
That lowers the level so nothing runs out of the thermo housing when you crack it.
The drained coolant can then be poured it back in later
with the car still raised and you shouldn't have to re-bleed the system.