Perfect - do your best to make the floors as even as new construction.

.- It costs me me less to turn over my 1500 SF units that rent for $3k/m then it does the same size section 8 unit because the property is cared for better and experiences less  wear and tear while fixed costs like cleaning and painting are easier to absorb. 

You can point out spots like nail holes where they hung pictures, dirty spots in the apartment needing cleaning, blown outlets they are overusing, etc.

For rentals, would a single floor or two floors makes sense? 

Easy to clean and safe. 

I know hosts have included additional cleaning fees for violations as a deterrent.If none of these solutions work, you could look into completely independent HVAC systems for the two units, though that would be a bigger upfront investment.

Kitchens, flooring, windows, doors, etc.? 

Some more than others. two units had wood floors that we kept.

It sounds like the 2 BR floor plan makes this process even more difficult.

I'd also look into property taxes and what is included with that $800 condo fee (that is really high though guessing it may include weekly cleaning).