When appraising a tri-level residence where about half of the height of the lower level is exposed and has one or more windows large enough to allow one or two rooms in the lower level to legally serve as bedrooms, should the appraiser be including the room count and square footage of those rooms in living area square footage, or is it not included because it is not totally above grade?

Usually the local zoning, building or health codes establish minimum requirements for bedrooms. Same thing for living space. It is not a one size fits all determination countrywide. Contact your local realty board - they might be able to assist you.