Most of the coop/roost/run designs I have seen do have the "sleeping area" (roost??) up off the ground and with doors to close and ventilation.
The reason you see this (and it's technically a coop above an extended run) is generally in a limited space, you want to maximize run space as much as possible, so by shortening the coop and moving it up you can use the space under it as part of the run.
If you don't have a shortage of space/budget, I feel a walk-in coop is the way to go - easier to get inside to maintain and the taller walls give you a LOT more space for adding ventilation.