what about a "2 story" coop. Pic below is a stock pic of the coop we have. What if I make the entire bottom undeneath the coop another "level" of the coop. Open up the whole thing so it's one big unit, add some more roosting bars, etc. Since we'd be expanding the run itself we really don't need the underneath.
The coop is mostly in the shade so using underneath to get out of the sun isn't an issue
The biggest issue I see with your idea is that chickens don't think that way. Assuming your chickens are all well integrated with each other, they'll want to stay together, so either you'll have all the chickens up, or all down.
What you can do for time being is to open up the whole thing as one unit, period. No upstairs part. Run roost lengthwise or maybe 2 across shorter side? This gives them the ventilation and light they need, plus space. You will probably still need to expand in the future, but while they're still small, at least that gives them a little more wiggle room.